eBay:iPads:: sold classification:: oobsmpl
bdanalytics
Date: (Fri) Jul 17, 2015
Introduction:
Data: Source: Training: https://inclass.kaggle.com/c/15-071x-the-analytics-edge-summer-2015/download/eBayiPadTrain.csv
New: https://inclass.kaggle.com/c/15-071x-the-analytics-edge-summer-2015/download/eBayiPadTest.csv
Time period:
Synopsis:
Based on analysis utilizing <> techniques,
Regression results: First run:
Classification results: template: prdline.my == “Unknown” -> 296 Low.cor.X.glm: Leaderboard: 0.83458 newobs_tbl=[N=471, Y=327]; submit_filename=template_Final_glm_submit.csv OOB_conf_mtrx=[YN=125, NY=76]=201; max.Accuracy.OOB=0.7710; opt.prob.threshold.OOB=0.6 startprice=100.00; biddable=95.42; productline=49.22; D.T.like=29.75; D.T.use=26.32; D.T.box=21.53;
prdline: -> Worse than template prdline.my == “Unknown” -> 285 All.X.no.rnorm.rf: Leaderboard: 0.82649 newobs_tbl=[N=485, Y=313]; submit_filename=prdline_Final_rf_submit.csv OOB_conf_mtrx=[YN=119, NY=80]=199; max.Accuracy.OOB=0.8339; opt.prob.threshold.OOB=0.5 startprice=100.00; biddable=84.25; D.sum.TfIdf=7.28; D.T.use=4.26; D.T.veri=2.78; D.T.scratch=1.99; D.T.box=; D.T.like=; Low.cor.X.glm: Leaderboard: 0.81234 newobs_tbl=[N=471, Y=327]; submit_filename=prdline_Low_cor_X_glm_submit.csv OOB_conf_mtrx=[YN=125, NY=74]=199; max.Accuracy.OOB=0.8205; opt.prob.threshold.OOB=0.6 startprice=100.00; biddable=96.07; prdline.my=51.37; D.T.like=29.39; D.T.use=25.43; D.T.box=22.27; D.T.veri=; D.T.scratch=;
oobssmpl: -> Low.cor.X.glm: Leaderboard: newobs_tbl=[N=440, Y=358]; submit_filename=oobsmpl_Final_glm_submit OOB_conf_mtrx=[YN=114, NY=84]=198; max.Accuracy.OOB=0.7780; opt.prob.threshold.OOB=0.5 startprice=100.00; biddable=93.87; prdline.my=60.48; D.sum.TfIdf=; D.T.condition=8.69; D.T.screen=7.96; D.T.use=7.50; D.T.veri=; D.T.scratch=;
Prediction Accuracy Enhancement Options:
- import.data chunk:
- which obs should be in fit vs. OOB (currently dirty.0 vs .1 is split 50%)
- inspect.data chunk:
- For date variables
- Appropriate factors ?
- Different / More last* features ?
- For date variables
- scrub.data chunk:
- transform.data chunk:
- derive features from multiple features
- manage.missing.data chunk:
- Not fill missing vars
- Fill missing numerics with a different algorithm
- Fill missing chars with data based on clusters
- extract.features chunk:
- Text variables: move to date extraction chunk ???
- Mine acronyms
- Mine places
- Text variables: move to date extraction chunk ???
- Review set_global_options chunk after features are finalized
[](.png)
Potential next steps include:
- Organization:
- Categorize by chunk
- Priority criteria:
- Ease of change
- Impacts report
- Cleans innards
- Bug report
- all chunks:
- at chunk-end rm(!glb_)
- manage.missing.data chunk:
- cleaner way to manage re-splitting of training vs. new entity
- extract.features chunk:
- Add n-grams for glb_txt_vars
- “RTextTools”, “tau”, “RWeka”, and “textcat” packages
- Convert user-specified mutate code to config specs
- Add n-grams for glb_txt_vars
- fit.models chunk:
- Prediction accuracy scatter graph:
- Add tiles (raw vs. PCA)
- Use shiny for drop-down of “important” features
Use plot.ly for interactive plots ?
- Change .fit suffix of model metrics to .mdl if it’s data independent (e.g. AIC, Adj.R.Squared - is it truly data independent ?, etc.)
- move model_type parameter to myfit_mdl before indep_vars_vctr (keep all model_* together)
- create a custom model for rpart that has minbucket as a tuning parameter
varImp for randomForest crashes in caret version:6.0.41 -> submit bug report
- Probability handling for multinomials vs. desired binomial outcome
- ROCR currently supports only evaluation of binary classification tasks (version 1.0.7)
extensions toward multiclass classification are scheduled for the next release
- Skip trControl.method=“cv” for dummy classifier ?
- Add custom model to caret for a dummy (baseline) classifier (binomial & multinomial) that generates proba/outcomes which mimics the freq distribution of glb_rsp_var values; Right now glb_dmy_glm_mdl always generates most frequent outcome in training data
glm_dmy_mdl should use the same method as glm_sel_mdl until custom dummy classifer is implemented
- fit.all.training chunk:
- myplot_prediction_classification: displays ‘x’ instead of ‘+’ when there are no prediction errors
- Compare glb_sel_mdl vs. glb_fin_mdl:
- varImp
- Prediction differences (shd be minimal ?)
- Move glb_analytics_diag_plots to mydsutils.R: (+) Easier to debug (-) Too many glb vars used
- Add print(ggplot.petrinet(glb_analytics_pn) + coord_flip()) at the end of every major chunk
- Parameterize glb_analytics_pn
- Move glb_impute_missing_data to mydsutils.R: (-) Too many glb vars used; glb_<>_df reassigned
- Replicate myfit_mdl_classification features in myfit_mdl_regression
- Do non-glm methods handle interaction terms ?
- f-score computation for classifiers should be summation across outcomes (not just the desired one ?)
- Add accuracy computation to glb_dmy_mdl in predict.data.new chunk
- Why does splitting fit.data.training.all chunk into separate chunks add an overhead of ~30 secs ? It’s not rbind b/c other chunks have lower elapsed time. Is it the number of plots ?
- Incorporate code chunks in print_sessionInfo
- Test against
- projects in github.com/bdanalytics
- lectures in jhu-datascience track
Analysis:
rm(list=ls())
set.seed(12345)
options(stringsAsFactors=FALSE)
source("~/Dropbox/datascience/R/myscript.R")
source("~/Dropbox/datascience/R/mydsutils.R")## Loading required package: caret
## Loading required package: lattice
## Loading required package: ggplot2source("~/Dropbox/datascience/R/myplot.R")
source("~/Dropbox/datascience/R/mypetrinet.R")
source("~/Dropbox/datascience/R/myplclust.R")
# Gather all package requirements here
suppressPackageStartupMessages(require(doMC))
registerDoMC(4) # max(length(glb_txt_vars), glb_n_cv_folds) + 1
#packageVersion("tm")
#require(sos); findFn("cosine", maxPages=2, sortby="MaxScore")
# Analysis control global variables
glb_trnng_url <- "https://inclass.kaggle.com/c/15-071x-the-analytics-edge-summer-2015/download/eBayiPadTrain.csv"
glb_newdt_url <- "https://inclass.kaggle.com/c/15-071x-the-analytics-edge-summer-2015/download/eBayiPadTest.csv"
glb_out_pfx <- "oobsmpl_"
glb_save_envir <- FALSE # or TRUE
glb_is_separate_newobs_dataset <- TRUE # or TRUE
glb_split_entity_newobs_datasets <- TRUE # or FALSE
glb_split_newdata_method <- "sample" # "condition" or "sample" or "copy"
glb_split_newdata_condition <- NULL # or "is.na(<var>)"; "<var> <condition_operator> <value>"
glb_split_newdata_size_ratio <- 0.3 # > 0 & < 1
glb_split_sample.seed <- 123 # or any integer
glb_max_fitobs <- NULL # or any integer
glb_is_regression <- FALSE; glb_is_classification <- !glb_is_regression;
glb_is_binomial <- TRUE #or FALSE
glb_rsp_var_raw <- "sold"
# for classification, the response variable has to be a factor
glb_rsp_var <- "sold.fctr"
# if the response factor is based on numbers/logicals e.g (0/1 OR TRUE/FALSE vs. "A"/"B"),
# or contains spaces (e.g. "Not in Labor Force")
# caret predict(..., type="prob") crashes
glb_map_rsp_raw_to_var <- function(raw) {
# return(log(raw))
ret_vals <- rep_len(NA, length(raw)); ret_vals[!is.na(raw)] <- ifelse(raw[!is.na(raw)] == 1, "Y", "N"); return(relevel(as.factor(ret_vals), ref="N"))
# #as.factor(paste0("B", raw))
# #as.factor(gsub(" ", "\\.", raw))
}
glb_map_rsp_raw_to_var(c(1, 1, 0, 0, NA))## [1] Y Y N N <NA>
## Levels: N Yglb_map_rsp_var_to_raw <- function(var) {
# return(exp(var))
as.numeric(var) - 1
# #as.numeric(var)
# #gsub("\\.", " ", levels(var)[as.numeric(var)])
# c("<=50K", " >50K")[as.numeric(var)]
# #c(FALSE, TRUE)[as.numeric(var)]
}
glb_map_rsp_var_to_raw(glb_map_rsp_raw_to_var(c(1, 1, 0, 0, NA)))## [1] 1 1 0 0 NAif ((glb_rsp_var != glb_rsp_var_raw) & is.null(glb_map_rsp_raw_to_var))
stop("glb_map_rsp_raw_to_var function expected")
glb_rsp_var_out <- paste0(glb_rsp_var, ".predict.") # model_id is appended later
# List info gathered for various columns
# <col_name>: <description>; <notes>
# description = The text description of the product provided by the seller.
# biddable = Whether this is an auction (biddable=1) or a sale with a fixed price (biddable=0).
# startprice = The start price (in US Dollars) for the auction (if biddable=1) or the sale price (if biddable=0).
# condition = The condition of the product (new, used, etc.)
# cellular = Whether the iPad has cellular connectivity (cellular=1) or not (cellular=0).
# carrier = The cellular carrier for which the iPad is equipped (if cellular=1); listed as "None" if cellular=0.
# color = The color of the iPad.
# storage = The iPad's storage capacity (in gigabytes).
# productline = The name of the product being sold.
# If multiple vars are parts of id, consider concatenating them to create one id var
# If glb_id_var == NULL, ".rownames <- row.names()" is the default
glb_id_var <- c("UniqueID")
glb_category_vars <- c("prdline.my")
glb_drop_vars <- c(NULL) # or c("<col_name>")
glb_map_vars <- NULL # or c("<var1>", "<var2>")
glb_map_urls <- list();
# glb_map_urls[["<var1>"]] <- "<var1.url>"
glb_assign_pairs_lst <- NULL;
# glb_assign_pairs_lst[["<var1>"]] <- list(from=c(NA),
# to=c("NA.my"))
glb_assign_vars <- names(glb_assign_pairs_lst)
# Derived features
glb_derive_lst <- NULL;
# Add logs of numerics that are not distributed normally -> do automatically ???
glb_derive_lst[["prdline.my"]] <- list(
mapfn=function(productline) { return(productline) }
, args=c("productline"))
# mapfn=function(Rasmussen) { return(ifelse(sign(Rasmussen) >= 0, 1, 0)) }
# mapfn=function(PropR) { return(as.factor(ifelse(PropR >= 0.5, "Y", "N"))) }
# mapfn=function(purpose) { return(relevel(as.factor(purpose), ref="all_other")) }
# mapfn=function(Week) { return(substr(Week, 1, 10)) }
# mapfn=function(raw) { tfr_raw <- as.character(cut(raw, 5));
# tfr_raw[is.na(tfr_raw)] <- "NA.my";
# return(as.factor(tfr_raw)) }
# , args=c("raw"))
# mapfn=function(PTS, oppPTS) { return(PTS - oppPTS) }
# , args=c("PTS", "oppPTS"))
# # If glb_allobs_df is not sorted in the desired manner
# mapfn=function(Week) { return(coredata(lag(zoo(orderBy(~Week, glb_allobs_df)$ILI), -2, na.pad=TRUE))) }
# mapfn=function(ILI) { return(coredata(lag(zoo(ILI), -2, na.pad=TRUE))) }
# mapfn=function(ILI.2.lag) { return(log(ILI.2.lag)) }
# glb_derive_lst[["<txt_var>.niso8859.log"]] <- list(
# mapfn=function(<txt_var>) { match_lst <- gregexpr("&#[[:digit:]]{3};", <txt_var>)
# match_num_vctr <- unlist(lapply(match_lst,
# function(elem) length(elem)))
# return(log(1 + match_num_vctr)) }
# , args=c("<txt_var>"))
# mapfn=function(raw) { mod_raw <- raw;
# mod_raw <- gsub("&#[[:digit:]]{3};", " ", mod_raw);
# # Modifications for this exercise only
# mod_raw <- gsub("\\bgoodIn ", "good In", mod_raw);
# return(mod_raw)
# # Create user-specified pattern vectors
# #sum(mycount_pattern_occ("Metropolitan Diary:", glb_allobs_df$Abstract) > 0)
# if (txt_var %in% c("Snippet", "Abstract")) {
# txt_X_df[, paste0(txt_var_pfx, ".P.metropolitan.diary.colon")] <-
# as.integer(0 + mycount_pattern_occ("Metropolitan Diary:",
# glb_allobs_df[, txt_var]))
#summary(glb_allobs_df[ ,grep("P.on.this.day", names(glb_allobs_df), value=TRUE)])
# glb_derive_lst[["<var1>"]] <- glb_derive_lst[["<var2>"]]
glb_derive_vars <- names(glb_derive_lst)
# tst <- "PropR.fctr"; args_lst <- NULL; for (arg in glb_derive_lst[[tst]]$args) args_lst[[arg]] <- glb_allobs_df[, arg]; print(head(args_lst[[arg]])); print(head(drv_vals <- do.call(glb_derive_lst[[tst]]$mapfn, args_lst)));
# print(which_ix <- which(args_lst[[arg]] == 0.75)); print(drv_vals[which_ix]);
glb_date_vars <- NULL # or c("<date_var>")
glb_date_fmts <- list(); #glb_date_fmts[["<date_var>"]] <- "%m/%e/%y"
glb_date_tzs <- list(); #glb_date_tzs[["<date_var>"]] <- "America/New_York"
#grep("America/New", OlsonNames(), value=TRUE)
glb_txt_vars <- c("description")
#Sys.setlocale("LC_ALL", "C") # For english
glb_txt_munge_filenames_pfx <- "mytxt_"
glb_append_stop_words <- list()
# Remember to use unstemmed words
#orderBy(~ -cor.y.abs, subset(glb_feats_df, grepl("[HSA]\\.T\\.", id) & !is.na(cor.high.X)))
#dsp_obs(Headline.contains="polit")
#subset(glb_allobs_df, H.T.compani > 0)[, c("UniqueID", "Headline", "H.T.compani")]
# glb_append_stop_words[["<txt_var1>"]] <- c(NULL
# # ,"<word1>" # <reason1>
# )
#subset(glb_allobs_df, S.T.newyorktim > 0)[, c("UniqueID", "Snippet", "S.T.newyorktim")]
#glb_txt_lst[["Snippet"]][which(glb_allobs_df$UniqueID %in% c(8394, 8317, 8339, 8350, 8307))]
glb_important_terms <- list()
# Remember to use stemmed terms
glb_sprs_thresholds <- c(0.950) # Generates ??? terms
# Properties:
# numrows(glb_feats_df) << numrows(glb_fitobs_df)
# Select terms that appear in at least 0.2 * O(FP/FN(glb_OOBobs_df))
# numrows(glb_OOBobs_df) = 1.1 * numrows(glb_newobs_df)
names(glb_sprs_thresholds) <- glb_txt_vars
# User-specified exclusions
glb_exclude_vars_as_features <- c("productline")
if (glb_rsp_var_raw != glb_rsp_var)
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
glb_rsp_var_raw)
# List feats that shd be excluded due to known causation by prediction variable
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
c(NULL)) # or c("<col_name>")
glb_impute_na_data <- FALSE # or TRUE
glb_mice_complete.seed <- 144 # or any integer
glb_cluster <- FALSE # or TRUE
glb_interaction_only_features <- NULL # or ???
glb_models_lst <- list(); glb_models_df <- data.frame()
# Regression
if (glb_is_regression)
glb_models_method_vctr <- c("lm", "glm", "bayesglm", "rpart", "rf") else
# Classification
if (glb_is_binomial)
glb_models_method_vctr <- c("glm", "bayesglm", "rpart", "rf") else
glb_models_method_vctr <- c("rpart", "rf")
# Baseline prediction model feature(s)
glb_Baseline_mdl_var <- NULL # or c("<col_name>")
glb_model_metric_terms <- NULL # or matrix(c(
# 0,1,2,3,4,
# 2,0,1,2,3,
# 4,2,0,1,2,
# 6,4,2,0,1,
# 8,6,4,2,0
# ), byrow=TRUE, nrow=5)
glb_model_metric <- NULL # or "<metric_name>"
glb_model_metric_maximize <- NULL # or FALSE (TRUE is not the default for both classification & regression)
glb_model_metric_smmry <- NULL # or function(data, lev=NULL, model=NULL) {
# confusion_mtrx <- t(as.matrix(confusionMatrix(data$pred, data$obs)))
# #print(confusion_mtrx)
# #print(confusion_mtrx * glb_model_metric_terms)
# metric <- sum(confusion_mtrx * glb_model_metric_terms) / nrow(data)
# names(metric) <- glb_model_metric
# return(metric)
# }
glb_tune_models_df <-
rbind(
#data.frame(parameter="cp", min=0.00005, max=0.00005, by=0.000005),
#seq(from=0.01, to=0.01, by=0.01)
#data.frame(parameter="mtry", min=080, max=100, by=10),
#data.frame(parameter="mtry", min=08, max=10, by=1),
data.frame(parameter="dummy", min=2, max=4, by=1)
)
# or NULL
glb_n_cv_folds <- 3 # or NULL
glb_clf_proba_threshold <- NULL # 0.5
# Model selection criteria
if (glb_is_regression)
glb_model_evl_criteria <- c("min.RMSE.OOB", "max.R.sq.OOB", "max.Adj.R.sq.fit")
if (glb_is_classification) {
if (glb_is_binomial)
glb_model_evl_criteria <-
c("max.Accuracy.OOB", "max.auc.OOB", "max.Kappa.OOB", "min.aic.fit") else
glb_model_evl_criteria <- c("max.Accuracy.OOB", "max.Kappa.OOB")
}
glb_sel_mdl_id <- NULL #"Low.cor.X.glm"
glb_fin_mdl_id <- glb_sel_mdl_id # or "Final"
# Depict process
glb_analytics_pn <- petrinet(name="glb_analytics_pn",
trans_df=data.frame(id=1:6,
name=c("data.training.all","data.new",
"model.selected","model.final",
"data.training.all.prediction","data.new.prediction"),
x=c( -5,-5,-15,-25,-25,-35),
y=c( -5, 5, 0, 0, -5, 5)
),
places_df=data.frame(id=1:4,
name=c("bgn","fit.data.training.all","predict.data.new","end"),
x=c( -0, -20, -30, -40),
y=c( 0, 0, 0, 0),
M0=c( 3, 0, 0, 0)
),
arcs_df=data.frame(
begin=c("bgn","bgn","bgn",
"data.training.all","model.selected","fit.data.training.all",
"fit.data.training.all","model.final",
"data.new","predict.data.new",
"data.training.all.prediction","data.new.prediction"),
end =c("data.training.all","data.new","model.selected",
"fit.data.training.all","fit.data.training.all","model.final",
"data.training.all.prediction","predict.data.new",
"predict.data.new","data.new.prediction",
"end","end")
))
#print(ggplot.petrinet(glb_analytics_pn))
print(ggplot.petrinet(glb_analytics_pn) + coord_flip())## Loading required package: grid
glb_analytics_avl_objs <- NULL
glb_chunks_df <- myadd_chunk(NULL, "import.data")## label step_major step_minor bgn end elapsed
## 1 import.data 1 0 9.832 NA NAStep 1.0: import data
chunk option: eval=
#glb_chunks_df <- myadd_chunk(NULL, "import.data")
glb_trnobs_df <- myimport_data(url=glb_trnng_url, comment="glb_trnobs_df",
force_header=TRUE)## [1] "Reading file ./data/eBayiPadTrain.csv..."
## [1] "dimensions of data in ./data/eBayiPadTrain.csv: 1,861 rows x 11 cols"
## description
## 1 iPad is in 8.5+ out of 10 cosmetic condition!
## 2 Previously used, please read description. May show signs of use such as scratches to the screen and
## 3
## 4
## 5 Please feel free to buy. All products have been thoroughly inspected, cleaned and tested to be 100%
## 6
## biddable startprice condition cellular carrier color
## 1 0 159.99 Used 0 None Black
## 2 1 0.99 Used 1 Verizon Unknown
## 3 0 199.99 Used 0 None White
## 4 0 235.00 New other (see details) 0 None Unknown
## 5 0 199.99 Seller refurbished Unknown Unknown Unknown
## 6 1 175.00 Used 1 AT&T Space Gray
## storage productline sold UniqueID
## 1 16 iPad 2 0 10001
## 2 16 iPad 2 1 10002
## 3 16 iPad 4 1 10003
## 4 16 iPad mini 2 0 10004
## 5 Unknown Unknown 0 10005
## 6 32 iPad mini 2 1 10006
## description
## 65
## 283 Pristine condition, comes with a case and stylus.
## 948 \x89\xdb\xcfUsed Apple Ipad 16 gig 1st generation in Great working condition and 100% functional.Very little
## 1354
## 1366 Item still in complete working order, minor scratches, normal wear and tear but no damage. screen is
## 1840
## biddable startprice condition cellular carrier color
## 65 0 195.00 Used 0 None Unknown
## 283 1 20.00 Used 0 None Unknown
## 948 0 110.00 Seller refurbished 0 None Black
## 1354 0 300.00 Used 0 None White
## 1366 1 125.00 Used Unknown Unknown Unknown
## 1840 0 249.99 Used 1 Sprint Space Gray
## storage productline sold UniqueID
## 65 16 iPad mini 0 10065
## 283 64 iPad 1 0 10283
## 948 32 iPad 1 0 10948
## 1354 16 iPad Air 1 11354
## 1366 Unknown iPad 1 1 11366
## 1840 16 iPad Air 1 11840
## description
## 1856 Overall item is in good condition and is fully operational and ready to use. Comes with box and
## 1857 Used. Tested. Guaranteed to work. Physical condition grade B+ does have some light scratches and
## 1858 This item is brand new and was never used; however, the box and/or packaging has been opened.
## 1859
## 1860 This unit has minor scratches on case and several small scratches on the display. \nIt is in
## 1861 30 Day Warranty. Fully functional engraved iPad 1st Generation with signs of normal wear which
## biddable startprice condition cellular carrier
## 1856 0 89.50 Used 1 AT&T
## 1857 0 239.95 Used 0 None
## 1858 0 329.99 New other (see details) 0 None
## 1859 0 400.00 New 0 None
## 1860 0 89.00 Seller refurbished 0 None
## 1861 0 119.99 Used 1 AT&T
## color storage productline sold UniqueID
## 1856 Unknown 16 iPad 1 0 11856
## 1857 Black 32 iPad 4 1 11857
## 1858 Space Gray 16 iPad Air 0 11858
## 1859 Gold 16 iPad mini 3 0 11859
## 1860 Black 64 iPad 1 1 11860
## 1861 Black 64 iPad 1 0 11861
## 'data.frame': 1861 obs. of 11 variables:
## $ description: chr "iPad is in 8.5+ out of 10 cosmetic condition!" "Previously used, please read description. May show signs of use such as scratches to the screen and " "" "" ...
## $ biddable : int 0 1 0 0 0 1 1 0 1 1 ...
## $ startprice : num 159.99 0.99 199.99 235 199.99 ...
## $ condition : chr "Used" "Used" "Used" "New other (see details)" ...
## $ cellular : chr "0" "1" "0" "0" ...
## $ carrier : chr "None" "Verizon" "None" "None" ...
## $ color : chr "Black" "Unknown" "White" "Unknown" ...
## $ storage : chr "16" "16" "16" "16" ...
## $ productline: chr "iPad 2" "iPad 2" "iPad 4" "iPad mini 2" ...
## $ sold : int 0 1 1 0 0 1 1 0 1 1 ...
## $ UniqueID : int 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010 ...
## - attr(*, "comment")= chr "glb_trnobs_df"
## NULL# glb_trnobs_df <- read.delim("data/hygiene.txt", header=TRUE, fill=TRUE, sep="\t",
# fileEncoding='iso-8859-1')
# glb_trnobs_df <- read.table("data/hygiene.dat.labels", col.names=c("dirty"),
# na.strings="[none]")
# glb_trnobs_df$review <- readLines("data/hygiene.dat", n =-1)
# comment(glb_trnobs_df) <- "glb_trnobs_df"
# glb_trnobs_df <- data.frame()
# for (symbol in c("Boeing", "CocaCola", "GE", "IBM", "ProcterGamble")) {
# sym_trnobs_df <-
# myimport_data(url=gsub("IBM", symbol, glb_trnng_url), comment="glb_trnobs_df",
# force_header=TRUE)
# sym_trnobs_df$Symbol <- symbol
# glb_trnobs_df <- myrbind_df(glb_trnobs_df, sym_trnobs_df)
# }
# glb_trnobs_df <-
# glb_trnobs_df %>% dplyr::filter(Year >= 1999)
if (glb_is_separate_newobs_dataset) {
glb_newobs_df <- myimport_data(url=glb_newdt_url, comment="glb_newobs_df",
force_header=TRUE)
# To make plots / stats / checks easier in chunk:inspectORexplore.data
glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df);
comment(glb_allobs_df) <- "glb_allobs_df"
} else {
glb_allobs_df <- glb_trnobs_df; comment(glb_allobs_df) <- "glb_allobs_df"
if (!glb_split_entity_newobs_datasets) {
stop("Not implemented yet")
glb_newobs_df <- glb_trnobs_df[sample(1:nrow(glb_trnobs_df),
max(2, nrow(glb_trnobs_df) / 1000)),]
} else if (glb_split_newdata_method == "condition") {
glb_newobs_df <- do.call("subset",
list(glb_trnobs_df, parse(text=glb_split_newdata_condition)))
glb_trnobs_df <- do.call("subset",
list(glb_trnobs_df, parse(text=paste0("!(",
glb_split_newdata_condition,
")"))))
} else if (glb_split_newdata_method == "sample") {
require(caTools)
set.seed(glb_split_sample.seed)
split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw],
SplitRatio=(1-glb_split_newdata_size_ratio))
glb_newobs_df <- glb_trnobs_df[!split, ]
glb_trnobs_df <- glb_trnobs_df[split ,]
} else if (glb_split_newdata_method == "copy") {
glb_trnobs_df <- glb_allobs_df
comment(glb_trnobs_df) <- "glb_trnobs_df"
glb_newobs_df <- glb_allobs_df
comment(glb_newobs_df) <- "glb_newobs_df"
} else stop("glb_split_newdata_method should be %in% c('condition', 'sample', 'copy')")
comment(glb_newobs_df) <- "glb_newobs_df"
myprint_df(glb_newobs_df)
str(glb_newobs_df)
if (glb_split_entity_newobs_datasets) {
myprint_df(glb_trnobs_df)
str(glb_trnobs_df)
}
} ## [1] "Reading file ./data/eBayiPadTest.csv..."
## [1] "dimensions of data in ./data/eBayiPadTest.csv: 798 rows x 10 cols"
## description
## 1 like new
## 2 Item is in great shape. I upgraded to the iPad Air 2 and don't need the mini any longer, even though
## 3 This iPad is working and is tested 100%. It runs great. It is in good condition. Cracked digitizer.
## 4
## 5 Grade A condition means that the Ipad is 100% working condition. Cosmetically 8/9 out of 10 - Will
## 6 Brand new factory sealed iPad in an OPEN BOX...THE BOX ITSELF IS HEAVILY DISTRESSED(see
## biddable startprice condition cellular carrier color
## 1 0 105.00 Used 1 AT&T Unknown
## 2 0 195.00 Used 0 None Unknown
## 3 0 219.99 Used 0 None Unknown
## 4 1 100.00 Used 0 None Unknown
## 5 0 210.99 Manufacturer refurbished 0 None Black
## 6 0 514.95 New other (see details) 0 None Gold
## storage productline UniqueID
## 1 32 iPad 1 11862
## 2 16 iPad mini 2 11863
## 3 64 iPad 3 11864
## 4 16 iPad mini 11865
## 5 32 iPad 3 11866
## 6 64 iPad Air 2 11867
## description
## 1 like new
## 142 iPad mini 1st gen wi-fi 16gb is in perfect working order.
## 309 In excellent condition. Minor scratches on the back. Screen in mint condition. Comes in original
## 312 iPad is in Great condition, the screen is in great condition showing only a few minor scratches, the
## 320 Good condition and fully functional
## 369
## biddable startprice condition cellular carrier color storage
## 1 0 105.00 Used 1 AT&T Unknown 32
## 142 1 0.99 Used 0 None Unknown 16
## 309 0 200.00 Used 1 AT&T Black 32
## 312 1 0.99 Used 0 None Unknown 16
## 320 1 60.00 Used 0 None White 16
## 369 1 197.97 Used 0 None Unknown 64
## productline UniqueID
## 1 iPad 1 11862
## 142 iPad mini 12003
## 309 iPad 3 12170
## 312 iPad mini 2 12173
## 320 iPad 1 12181
## 369 iPad mini 3 12230
## description
## 793 Crack on digitizer near top. Top line of digitizer does not respond to touch. Other than that, all
## 794
## 795
## 796
## 797
## 798 Slightly Used. Includes everything you need plus a nice leather case!\nThere is a slice mark on the
## biddable startprice condition cellular carrier color
## 793 0 104.00 For parts or not working 1 Unknown Black
## 794 0 95.00 Used 1 AT&T Unknown
## 795 1 199.99 Manufacturer refurbished 0 None White
## 796 0 149.99 Used 0 None Unknown
## 797 0 7.99 New Unknown Unknown Unknown
## 798 0 139.00 Used 1 Unknown Black
## storage productline UniqueID
## 793 16 iPad 2 12654
## 794 64 iPad 1 12655
## 795 16 iPad 4 12656
## 796 16 iPad 2 12657
## 797 Unknown iPad 3 12658
## 798 32 Unknown 12659
## 'data.frame': 798 obs. of 10 variables:
## $ description: chr "like new" "Item is in great shape. I upgraded to the iPad Air 2 and don't need the mini any longer, even though " "This iPad is working and is tested 100%. It runs great. It is in good condition. Cracked digitizer." "" ...
## $ biddable : int 0 0 0 1 0 0 0 0 0 1 ...
## $ startprice : num 105 195 220 100 211 ...
## $ condition : chr "Used" "Used" "Used" "Used" ...
## $ cellular : chr "1" "0" "0" "0" ...
## $ carrier : chr "AT&T" "None" "None" "None" ...
## $ color : chr "Unknown" "Unknown" "Unknown" "Unknown" ...
## $ storage : chr "32" "16" "64" "16" ...
## $ productline: chr "iPad 1" "iPad mini 2" "iPad 3" "iPad mini" ...
## $ UniqueID : int 11862 11863 11864 11865 11866 11867 11868 11869 11870 11871 ...
## - attr(*, "comment")= chr "glb_newobs_df"
## NULLif ((num_nas <- sum(is.na(glb_trnobs_df[, glb_rsp_var_raw]))) > 0)
stop("glb_trnobs_df$", glb_rsp_var_raw, " contains NAs for ", num_nas, " obs")
if (nrow(glb_trnobs_df) == nrow(glb_allobs_df))
warning("glb_trnobs_df same as glb_allobs_df")
if (nrow(glb_newobs_df) == nrow(glb_allobs_df))
warning("glb_newobs_df same as glb_allobs_df")
if (length(glb_drop_vars) > 0) {
warning("dropping vars: ", paste0(glb_drop_vars, collapse=", "))
glb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df), glb_drop_vars)]
glb_trnobs_df <- glb_trnobs_df[, setdiff(names(glb_trnobs_df), glb_drop_vars)]
glb_newobs_df <- glb_newobs_df[, setdiff(names(glb_newobs_df), glb_drop_vars)]
}
#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Combine trnent & newobs into glb_allobs_df for easier manipulation
glb_trnobs_df$.src <- "Train"; glb_newobs_df$.src <- "Test";
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, ".src")
glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df)
comment(glb_allobs_df) <- "glb_allobs_df"
# Check for duplicates in glb_id_var
if (length(glb_id_var) == 0) {
warning("using .rownames as identifiers for observations")
glb_allobs_df$.rownames <- rownames(glb_allobs_df)
glb_trnobs_df$.rownames <- rownames(subset(glb_allobs_df, .src == "Train"))
glb_newobs_df$.rownames <- rownames(subset(glb_allobs_df, .src == "Test"))
glb_id_var <- ".rownames"
}
if (sum(duplicated(glb_allobs_df[, glb_id_var, FALSE])) > 0)
stop(glb_id_var, " duplicated in glb_allobs_df")
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_id_var)
glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
glb_trnobs_df <- glb_newobs_df <- NULL
glb_chunks_df <- myadd_chunk(glb_chunks_df, "inspect.data", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 1 import.data 1 0 9.832 10.247 0.416
## 2 inspect.data 2 0 10.248 NA NAStep 2.0: inspect data
#print(str(glb_allobs_df))
#View(glb_allobs_df)
dsp_class_dstrb <- function(var) {
xtab_df <- mycreate_xtab_df(glb_allobs_df, c(".src", var))
rownames(xtab_df) <- xtab_df$.src
xtab_df <- subset(xtab_df, select=-.src)
print(xtab_df)
print(xtab_df / rowSums(xtab_df, na.rm=TRUE))
}
# Performed repeatedly in other chunks
glb_chk_data <- function() {
# Histogram of predictor in glb_trnobs_df & glb_newobs_df
print(myplot_histogram(glb_allobs_df, glb_rsp_var_raw) + facet_wrap(~ .src))
if (glb_is_classification)
dsp_class_dstrb(var=ifelse(glb_rsp_var %in% names(glb_allobs_df),
glb_rsp_var, glb_rsp_var_raw))
mycheck_problem_data(glb_allobs_df)
}
glb_chk_data()## stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
## stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
## Loading required package: reshape2
## sold.0 sold.1 sold.NA
## Test NA NA 798
## Train 1001 860 NA
## sold.0 sold.1 sold.NA
## Test NA NA 1
## Train 0.5378829 0.4621171 NA
## [1] "numeric data missing in glb_allobs_df: "
## sold
## 798
## [1] "numeric data w/ 0s in glb_allobs_df: "
## biddable sold
## 1446 1001
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## description condition cellular carrier color storage
## 1521 0 0 0 0 0
## productline
## 0# Create new features that help diagnostics
if (!is.null(glb_map_rsp_raw_to_var)) {
glb_allobs_df[, glb_rsp_var] <-
glb_map_rsp_raw_to_var(glb_allobs_df[, glb_rsp_var_raw])
mycheck_map_results(mapd_df=glb_allobs_df,
from_col_name=glb_rsp_var_raw, to_col_name=glb_rsp_var)
if (glb_is_classification) dsp_class_dstrb(glb_rsp_var)
}## Loading required package: sqldf
## Loading required package: gsubfn
## Loading required package: proto
## Loading required package: RSQLite
## Loading required package: DBI
## Loading required package: tcltk## sold sold.fctr .n
## 1 0 N 1001
## 2 1 Y 860
## 3 NA <NA> 798## Warning: Removed 1 rows containing missing values (position_stack).
## sold.fctr.N sold.fctr.Y sold.fctr.NA
## Test NA NA 798
## Train 1001 860 NA
## sold.fctr.N sold.fctr.Y sold.fctr.NA
## Test NA NA 1
## Train 0.5378829 0.4621171 NA# check distribution of all numeric data
dsp_numeric_feats_dstrb <- function(feats_vctr) {
for (feat in feats_vctr) {
print(sprintf("feat: %s", feat))
if (glb_is_regression)
gp <- myplot_scatter(df=glb_allobs_df, ycol_name=glb_rsp_var, xcol_name=feat,
smooth=TRUE)
if (glb_is_classification)
gp <- myplot_box(df=glb_allobs_df, ycol_names=feat, xcol_name=glb_rsp_var)
if (inherits(glb_allobs_df[, feat], "factor"))
gp <- gp + facet_wrap(reformulate(feat))
print(gp)
}
}
# dsp_numeric_vars_dstrb(setdiff(names(glb_allobs_df),
# union(myfind_chr_cols_df(glb_allobs_df),
# c(glb_rsp_var_raw, glb_rsp_var))))
add_new_diag_feats <- function(obs_df, ref_df=glb_allobs_df) {
require(plyr)
obs_df <- mutate(obs_df,
# <col_name>.NA=is.na(<col_name>),
# <col_name>.fctr=factor(<col_name>,
# as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))),
# <col_name>.fctr=relevel(factor(<col_name>,
# as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))),
# "<ref_val>"),
# <col2_name>.fctr=relevel(factor(ifelse(<col1_name> == <val>, "<oth_val>", "<ref_val>")),
# as.factor(c("R", "<ref_val>")),
# ref="<ref_val>"),
# This doesn't work - use sapply instead
# <col_name>.fctr_num=grep(<col_name>, levels(<col_name>.fctr)),
#
# Date.my=as.Date(strptime(Date, "%m/%d/%y %H:%M")),
# Year=year(Date.my),
# Month=months(Date.my),
# Weekday=weekdays(Date.my)
# <col_name>=<table>[as.character(<col2_name>)],
# <col_name>=as.numeric(<col2_name>),
# <col_name> = trunc(<col2_name> / 100),
.rnorm = rnorm(n=nrow(obs_df))
)
# If levels of a factor are different across obs_df & glb_newobs_df; predict.glm fails
# Transformations not handled by mutate
# obs_df$<col_name>.fctr.num <- sapply(1:nrow(obs_df),
# function(row_ix) grep(obs_df[row_ix, "<col_name>"],
# levels(obs_df[row_ix, "<col_name>.fctr"])))
#print(summary(obs_df))
#print(sapply(names(obs_df), function(col) sum(is.na(obs_df[, col]))))
return(obs_df)
}
glb_allobs_df <- add_new_diag_feats(glb_allobs_df)## Loading required package: plyrrequire(dplyr)## Loading required package: dplyr
##
## Attaching package: 'dplyr'
##
## The following objects are masked from 'package:plyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize
##
## The following objects are masked from 'package:stats':
##
## filter, lag
##
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Merge some <descriptor>
# glb_allobs_df$<descriptor>.my <- glb_allobs_df$<descriptor>
# glb_allobs_df[grepl("\\bAIRPORT\\b", glb_allobs_df$<descriptor>.my),
# "<descriptor>.my"] <- "AIRPORT"
# glb_allobs_df$<descriptor>.my <-
# plyr::revalue(glb_allobs_df$<descriptor>.my, c(
# "ABANDONED BUILDING" = "OTHER",
# "##" = "##"
# ))
# print(<descriptor>_freq_df <- mycreate_sqlxtab_df(glb_allobs_df, c("<descriptor>.my")))
# # print(dplyr::filter(<descriptor>_freq_df, grepl("(MEDICAL|DENTAL|OFFICE)", <descriptor>.my)))
# # print(dplyr::filter(dplyr::select(glb_allobs_df, -<var.zoo>),
# # grepl("STORE", <descriptor>.my)))
# glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, "<descriptor>")
# Check distributions of newly transformed / extracted vars
# Enhancement: remove vars that were displayed ealier
dsp_numeric_feats_dstrb(feats_vctr=setdiff(names(glb_allobs_df),
c(myfind_chr_cols_df(glb_allobs_df), glb_rsp_var_raw, glb_rsp_var,
glb_exclude_vars_as_features)))## [1] "feat: biddable"
## [1] "feat: startprice"
## [1] "feat: .rnorm"
# Convert factors to dummy variables
# Build splines require(splines); bsBasis <- bs(training$age, df=3)
#pairs(subset(glb_trnobs_df, select=-c(col_symbol)))
# Check for glb_newobs_df & glb_trnobs_df features range mismatches
# Other diagnostics:
# print(subset(glb_trnobs_df, <col1_name> == max(glb_trnobs_df$<col1_name>, na.rm=TRUE) &
# <col2_name> <= mean(glb_trnobs_df$<col1_name>, na.rm=TRUE)))
# print(glb_trnobs_df[which.max(glb_trnobs_df$<col_name>),])
# print(<col_name>_freq_glb_trnobs_df <- mycreate_tbl_df(glb_trnobs_df, "<col_name>"))
# print(which.min(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>)[, 2]))
# print(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>))
# print(table(is.na(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(table(sign(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(mycreate_xtab_df(glb_trnobs_df, <col1_name>))
# print(mycreate_xtab_df(glb_trnobs_df, c(<col1_name>, <col2_name>)))
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <-
# mycreate_xtab_df(glb_trnobs_df, c("<col1_name>", "<col2_name>")))
# <col1_name>_<col2_name>_xtab_glb_trnobs_df[is.na(<col1_name>_<col2_name>_xtab_glb_trnobs_df)] <- 0
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <-
# mutate(<col1_name>_<col2_name>_xtab_glb_trnobs_df,
# <col3_name>=(<col1_name> * 1.0) / (<col1_name> + <col2_name>)))
# print(mycreate_sqlxtab_df(glb_allobs_df, c("<col1_name>", "<col2_name>")))
# print(<col2_name>_min_entity_arr <-
# sort(tapply(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>, min, na.rm=TRUE)))
# print(<col1_name>_na_by_<col2_name>_arr <-
# sort(tapply(glb_trnobs_df$<col1_name>.NA, glb_trnobs_df$<col2_name>, mean, na.rm=TRUE)))
# Other plots:
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>"))
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>", xcol_name="<col2_name>"))
# print(myplot_line(subset(glb_trnobs_df, Symbol %in% c("CocaCola", "ProcterGamble")),
# "Date.POSIX", "StockPrice", facet_row_colnames="Symbol") +
# geom_vline(xintercept=as.numeric(as.POSIXlt("2003-03-01"))) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1983-01-01")))
# )
# print(myplot_line(subset(glb_trnobs_df, Date.POSIX > as.POSIXct("2004-01-01")),
# "Date.POSIX", "StockPrice") +
# geom_line(aes(color=Symbol)) +
# coord_cartesian(xlim=c(as.POSIXct("1990-01-01"),
# as.POSIXct("2000-01-01"))) +
# coord_cartesian(ylim=c(0, 250)) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1997-09-01"))) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1997-11-01")))
# )
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", colorcol_name="<Pred.fctr>") +
# geom_point(data=subset(glb_allobs_df, <condition>),
# mapping=aes(x=<x_var>, y=<y_var>), color="red", shape=4, size=5) +
# geom_vline(xintercept=84))
glb_chunks_df <- myadd_chunk(glb_chunks_df, "scrub.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 2 inspect.data 2 0 10.248 15.538 5.29
## 3 scrub.data 2 1 15.538 NA NAStep 2.1: scrub data
mycheck_problem_data(glb_allobs_df)## [1] "numeric data missing in glb_allobs_df: "
## sold sold.fctr
## 798 798
## [1] "numeric data w/ 0s in glb_allobs_df: "
## biddable sold
## 1446 1001
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## description condition cellular carrier color storage
## 1521 0 0 0 0 0
## productline
## 0dsp_catgs <- function() {
print("NewsDesk:")
print(table(glb_allobs_df$NewsDesk))
print("SectionName:")
print(table(glb_allobs_df$SectionName))
print("SubsectionName:")
print(table(glb_allobs_df$SubsectionName))
}
findOffendingCharacter <- function(x, maxStringLength=256){
print(x)
for (c in 1:maxStringLength){
offendingChar <- substr(x,c,c)
#print(offendingChar) #uncomment if you want the indiv characters printed
#the next character is the offending multibyte Character
}
}
# string_vector <- c("test", "Se\x96ora", "works fine")
# lapply(string_vector, findOffendingCharacter)
# lapply(glb_allobs_df$description[29], findOffendingCharacter)
sel_obs <- function(vars_lst, ignore.case=TRUE, perl=FALSE) {
tmp_df <- glb_allobs_df
# Does not work for Popular == NAs ???
# if (!is.null(Popular)) {
# if (is.na(Popular))
# tmp_df <- tmp_df[is.na(tmp_df$Popular), ] else
# tmp_df <- tmp_df[tmp_df$Popular == Popular, ]
# }
# if (!is.null(NewsDesk))
# tmp_df <- tmp_df[tmp_df$NewsDesk == NewsDesk, ]
for (var in names(vars_lst)) {
if (grepl(".contains", var))
tmp_df <- tmp_df[grep(vars_lst[var],
tmp_df[, unlist(strsplit(var, ".contains"))],
ignore.case=ignore.case, perl=perl), ]
else
tmp_df <- tmp_df[tmp_df[, var] == vars_lst[var], ]
}
return(glb_allobs_df[, glb_id_var] %in% tmp_df[, glb_id_var])
}
#print(glb_allobs_df[sel_obs(list(description.contains="mini(?!m)"), perl=TRUE), "description"])
dsp_obs <- function(..., cols=c(NULL), all=FALSE) {
tmp_df <- glb_allobs_df[sel_obs(...),
c(glb_id_var, glb_rsp_var, glb_category_vars, glb_txt_vars, cols),
FALSE]
if(all) { print(tmp_df) } else { myprint_df(tmp_df) }
}
#dsp_obs(list(description.contains="mini(?!m)"), perl=TRUE)
#dsp_obs(Popular=1, NewsDesk="", SectionName="", Headline.contains="Boehner")
# dsp_obs(Popular=1, NewsDesk="", SectionName="")
# dsp_obs(Popular=NA, NewsDesk="", SectionName="")
dsp_tbl <- function(...) {
tmp_entity_df <- glb_allobs_df[sel_obs(...), ]
tmp_tbl <- table(tmp_entity_df$NewsDesk,
tmp_entity_df$SectionName,
tmp_entity_df$SubsectionName,
tmp_entity_df$Popular, useNA="ifany")
#print(names(tmp_tbl))
#print(dimnames(tmp_tbl))
print(tmp_tbl)
}
dsp_hdlxtab <- function(str)
print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
c("Headline.pfx", "Headline", glb_rsp_var)))
#dsp_hdlxtab("(1914)|(1939)")
dsp_catxtab <- function(str)
print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
c("Headline.pfx", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# dsp_catxtab("1914)|(1939)")
# dsp_catxtab("19(14|39|64):")
# dsp_catxtab("19..:")
# Create myCategory <- NewsDesk#SectionName#SubsectionName
# Fix some data before merging categories
# glb_allobs_df[sel_obs(Headline.contains="Your Turn:", NewsDesk=""),
# "NewsDesk"] <- "Styles"
# glb_allobs_df[sel_obs(Headline.contains="School", NewsDesk="", SectionName="U.S.",
# SubsectionName=""),
# "SubsectionName"] <- "Education"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
# "SectionName"] <- "Business Day"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
# "SubsectionName"] <- "Small Business"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
# "SectionName"] <- "Opinion"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
# "SubsectionName"] <- "Room For Debate"
# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName="", Popular=NA),
# "SubsectionName"] <- "Small Business"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(7973),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName=""),
# "SectionName"] <- "Technology"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5076, 5736, 5924, 5911, 6532),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df[sel_obs(SectionName="Health"),
# "NewsDesk"] <- "Science"
# glb_allobs_df[sel_obs(SectionName="Travel"),
# "NewsDesk"] <- "Travel"
#
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
# "SectionName"] <- ""
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
# "SubsectionName"] <- ""
# glb_allobs_df[sel_obs(NewsDesk="Styles", SectionName="", SubsectionName="", Popular=1),
# "SectionName"] <- "U.S."
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5486),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df$myCategory <- paste(glb_allobs_df$NewsDesk,
# glb_allobs_df$SectionName,
# glb_allobs_df$SubsectionName,
# sep="#")
# dsp_obs( Headline.contains="Music:"
# #,NewsDesk=""
# #,SectionName=""
# #,SubsectionName="Fashion & Style"
# #,Popular=1 #NA
# ,cols= c("UniqueID", "Headline", "Popular", "myCategory",
# "NewsDesk", "SectionName", "SubsectionName"),
# all=TRUE)
# dsp_obs( Headline.contains="."
# ,NewsDesk=""
# ,SectionName="Opinion"
# ,SubsectionName=""
# #,Popular=1 #NA
# ,cols= c("UniqueID", "Headline", "Popular", "myCategory",
# "NewsDesk", "SectionName", "SubsectionName"),
# all=TRUE)
# Merge some categories
# glb_allobs_df$myCategory <-
# plyr::revalue(glb_allobs_df$myCategory, c(
# "#Business Day#Dealbook" = "Business#Business Day#Dealbook",
# "#Business Day#Small Business" = "Business#Business Day#Small Business",
# "#Crosswords/Games#" = "Business#Crosswords/Games#",
# "Business##" = "Business#Technology#",
# "#Open#" = "Business#Technology#",
# "#Technology#" = "Business#Technology#",
#
# "#Arts#" = "Culture#Arts#",
# "Culture##" = "Culture#Arts#",
#
# "#World#Asia Pacific" = "Foreign#World#Asia Pacific",
# "Foreign##" = "Foreign#World#",
#
# "#N.Y. / Region#" = "Metro#N.Y. / Region#",
#
# "#Opinion#" = "OpEd#Opinion#",
# "OpEd##" = "OpEd#Opinion#",
#
# "#Health#" = "Science#Health#",
# "Science##" = "Science#Health#",
#
# "Styles##" = "Styles##Fashion",
# "Styles#Health#" = "Science#Health#",
# "Styles#Style#Fashion & Style" = "Styles##Fashion",
#
# "#Travel#" = "Travel#Travel#",
#
# "Magazine#Magazine#" = "myOther",
# "National##" = "myOther",
# "National#U.S.#Politics" = "myOther",
# "Sports##" = "myOther",
# "Sports#Sports#" = "myOther",
# "#U.S.#" = "myOther",
#
#
# # "Business##Small Business" = "Business#Business Day#Small Business",
# #
# # "#Opinion#" = "#Opinion#Room For Debate",
# "##" = "##"
# # "Business##" = "Business#Business Day#Dealbook",
# # "Foreign#World#" = "Foreign##",
# # "#Open#" = "Other",
# # "#Opinion#The Public Editor" = "OpEd#Opinion#",
# # "Styles#Health#" = "Styles##",
# # "Styles#Style#Fashion & Style" = "Styles##",
# # "#U.S.#" = "#U.S.#Education",
# ))
# ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
# mycreate_sqlxtab_df(glb_allobs_df,
# c("myCategory", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# myprint_df(ctgry_xtab_df)
# write.table(ctgry_xtab_df, paste0(glb_out_pfx, "ctgry_xtab.csv"),
# row.names=FALSE)
# ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df,
# myCategory + NewsDesk + SectionName + SubsectionName ~
# Popular.fctr, sum, value.var=".n"))
# myprint_df(ctgry_cast_df)
# write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_cast.csv"),
# row.names=FALSE)
# print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df[, glb_rsp_var],
# useNA="ifany"))
dsp_chisq.test <- function(...) {
sel_df <- glb_allobs_df[sel_obs(...) &
!is.na(glb_allobs_df$Popular), ]
sel_df$.marker <- 1
ref_df <- glb_allobs_df[!is.na(glb_allobs_df$Popular), ]
mrg_df <- merge(ref_df[, c(glb_id_var, "Popular")],
sel_df[, c(glb_id_var, ".marker")], all.x=TRUE)
mrg_df[is.na(mrg_df)] <- 0
print(mrg_tbl <- table(mrg_df$.marker, mrg_df$Popular))
print("Rows:Selected; Cols:Popular")
#print(mrg_tbl)
print(chisq.test(mrg_tbl))
}
# dsp_chisq.test(Headline.contains="[Ee]bola")
# dsp_chisq.test(Snippet.contains="[Ee]bola")
# dsp_chisq.test(Abstract.contains="[Ee]bola")
# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola"), ],
# c(glb_rsp_var, "NewsDesk", "SectionName", "SubsectionName")))
# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName))
# print(table(glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))
# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))
# glb_allobs_df$myCategory.fctr <- as.factor(glb_allobs_df$myCategory)
# glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
# c("myCategory", "NewsDesk", "SectionName", "SubsectionName"))
# Copy Headline into Snipper & Abstract if they are empty
# print(glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, c("Headline", "Snippet")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Snippet,
# c("UniqueID", "Headline", "Snippet")])
# glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Snippet"] <-
# glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Headline"]
#
# print(glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, c("Headline", "Abstract")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Abstract,
# c("UniqueID", "Headline", "Abstract")])
# glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Abstract"] <-
# glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Headline"]
# WordCount_0_df <- subset(glb_allobs_df, WordCount == 0)
# table(WordCount_0_df$Popular, WordCount_0_df$WordCount, useNA="ifany")
# myprint_df(WordCount_0_df[,
# c("UniqueID", "Popular", "WordCount", "Headline")])Step 2.1: scrub data
glb_chunks_df <- myadd_chunk(glb_chunks_df, "transform.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 3 scrub.data 2 1 15.538 16.366 0.828
## 4 transform.data 2 2 16.367 NA NA### Mapping dictionary
#sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
if (!is.null(glb_map_vars)) {
for (feat in glb_map_vars) {
map_df <- myimport_data(url=glb_map_urls[[feat]],
comment="map_df",
print_diagn=TRUE)
glb_allobs_df <- mymap_codes(glb_allobs_df, feat, names(map_df)[2],
map_df, map_join_col_name=names(map_df)[1],
map_tgt_col_name=names(map_df)[2])
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_map_vars)
}
### Forced Assignments
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (feat in glb_assign_vars) {
new_feat <- paste0(feat, ".my")
print(sprintf("Forced Assignments for: %s -> %s...", feat, new_feat))
glb_allobs_df[, new_feat] <- glb_allobs_df[, feat]
pairs <- glb_assign_pairs_lst[[feat]]
for (pair_ix in 1:length(pairs$from)) {
if (is.na(pairs$from[pair_ix]))
nobs <- nrow(filter(glb_allobs_df,
is.na(eval(parse(text=feat),
envir=glb_allobs_df)))) else
nobs <- sum(glb_allobs_df[, feat] == pairs$from[pair_ix])
#nobs <- nrow(filter(glb_allobs_df, is.na(Married.fctr))) ; print(nobs)
if ((is.na(pairs$from[pair_ix])) && (is.na(pairs$to[pair_ix])))
stop("what are you trying to do ???")
if (is.na(pairs$from[pair_ix]))
glb_allobs_df[is.na(glb_allobs_df[, feat]), new_feat] <-
pairs$to[pair_ix] else
glb_allobs_df[glb_allobs_df[, feat] == pairs$from[pair_ix], new_feat] <-
pairs$to[pair_ix]
print(sprintf(" %s -> %s for %s obs",
pairs$from[pair_ix], pairs$to[pair_ix], format(nobs, big.mark=",")))
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_assign_vars)
}
### Derivations using mapping functions
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (new_feat in glb_derive_vars) {
print(sprintf("Creating new feature: %s...", new_feat))
args_lst <- NULL
for (arg in glb_derive_lst[[new_feat]]$args)
args_lst[[arg]] <- glb_allobs_df[, arg]
glb_allobs_df[, new_feat] <- do.call(glb_derive_lst[[new_feat]]$mapfn, args_lst)
}## [1] "Creating new feature: prdline.my..."Step 2.2: transform data
#```{r extract_features, cache=FALSE, eval=!is.null(glb_txt_vars)}
glb_chunks_df <- myadd_chunk(glb_chunks_df, "extract.features", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 4 transform.data 2 2 16.367 16.448 0.081
## 5 extract.features 3 0 16.448 NA NAextract.features_chunk_df <- myadd_chunk(NULL, "extract.features_bgn")## label step_major step_minor bgn end elapsed
## 1 extract.features_bgn 1 0 16.455 NA NA# Options:
# Select Tf, log(1 + Tf), Tf-IDF or BM25Tf-IDf
# Create new features that help prediction
# <col_name>.lag.2 <- lag(zoo(glb_trnobs_df$<col_name>), -2, na.pad=TRUE)
# glb_trnobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
# <col_name>.lag.2 <- lag(zoo(glb_newobs_df$<col_name>), -2, na.pad=TRUE)
# glb_newobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
#
# glb_newobs_df[1, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df) - 1,
# "<col_name>"]
# glb_newobs_df[2, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df),
# "<col_name>"]
# glb_allobs_df <- mutate(glb_allobs_df,
# A.P.http=ifelse(grepl("http",Added,fixed=TRUE), 1, 0)
# )
#
# glb_trnobs_df <- mutate(glb_trnobs_df,
# )
#
# glb_newobs_df <- mutate(glb_newobs_df,
# )
# Convert dates to numbers
# typically, dates come in as chars;
# so this must be done before converting chars to factors
#stop(here"); sav_allobs_df <- glb_allobs_df #; glb_allobs_df <- sav_allobs_df
if (!is.null(glb_date_vars)) {
glb_allobs_df <- cbind(glb_allobs_df,
myextract_dates_df(df=glb_allobs_df, vars=glb_date_vars,
id_vars=glb_id_var, rsp_var=glb_rsp_var))
for (sfx in c("", ".POSIX"))
glb_exclude_vars_as_features <-
union(glb_exclude_vars_as_features,
paste(glb_date_vars, sfx, sep=""))
for (feat in glb_date_vars) {
glb_allobs_df <- orderBy(reformulate(paste0(feat, ".POSIX")), glb_allobs_df)
# print(myplot_scatter(glb_allobs_df, xcol_name=paste0(feat, ".POSIX"),
# ycol_name=glb_rsp_var, colorcol_name=glb_rsp_var))
print(myplot_scatter(glb_allobs_df[glb_allobs_df[, paste0(feat, ".POSIX")] >=
strptime("2012-12-01", "%Y-%m-%d"), ],
xcol_name=paste0(feat, ".POSIX"),
ycol_name=glb_rsp_var, colorcol_name=paste0(feat, ".wkend")))
# Create features that measure the gap between previous timestamp in the data
require(zoo)
z <- zoo(as.numeric(as.POSIXlt(glb_allobs_df[, paste0(feat, ".POSIX")])))
glb_allobs_df[, paste0(feat, ".zoo")] <- z
print(head(glb_allobs_df[, c(glb_id_var, feat, paste0(feat, ".zoo"))]))
print(myplot_scatter(glb_allobs_df[glb_allobs_df[, paste0(feat, ".POSIX")] >
strptime("2012-10-01", "%Y-%m-%d"), ],
xcol_name=paste0(feat, ".zoo"), ycol_name=glb_rsp_var,
colorcol_name=glb_rsp_var))
b <- zoo(, seq(nrow(glb_allobs_df)))
last1 <- as.numeric(merge(z-lag(z, -1), b, all=TRUE)); last1[is.na(last1)] <- 0
glb_allobs_df[, paste0(feat, ".last1.log")] <- log(1 + last1)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last1.log")] > 0, ],
ycol_names=paste0(feat, ".last1.log"),
xcol_name=glb_rsp_var))
last2 <- as.numeric(merge(z-lag(z, -2), b, all=TRUE)); last2[is.na(last2)] <- 0
glb_allobs_df[, paste0(feat, ".last2.log")] <- log(1 + last2)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last2.log")] > 0, ],
ycol_names=paste0(feat, ".last2.log"),
xcol_name=glb_rsp_var))
last10 <- as.numeric(merge(z-lag(z, -10), b, all=TRUE)); last10[is.na(last10)] <- 0
glb_allobs_df[, paste0(feat, ".last10.log")] <- log(1 + last10)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last10.log")] > 0, ],
ycol_names=paste0(feat, ".last10.log"),
xcol_name=glb_rsp_var))
last100 <- as.numeric(merge(z-lag(z, -100), b, all=TRUE)); last100[is.na(last100)] <- 0
glb_allobs_df[, paste0(feat, ".last100.log")] <- log(1 + last100)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last100.log")] > 0, ],
ycol_names=paste0(feat, ".last100.log"),
xcol_name=glb_rsp_var))
glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
c(paste0(feat, ".zoo")))
# all2$last3 = as.numeric(merge(z-lag(z, -3), b, all = TRUE))
# all2$last5 = as.numeric(merge(z-lag(z, -5), b, all = TRUE))
# all2$last10 = as.numeric(merge(z-lag(z, -10), b, all = TRUE))
# all2$last20 = as.numeric(merge(z-lag(z, -20), b, all = TRUE))
# all2$last50 = as.numeric(merge(z-lag(z, -50), b, all = TRUE))
#
#
# # order table
# all2 = all2[order(all2$id),]
#
# ## fill in NAs
# # count averages
# na.avg = all2 %>% group_by(weekend, hour) %>% dplyr::summarise(
# last1=mean(last1, na.rm=TRUE),
# last3=mean(last3, na.rm=TRUE),
# last5=mean(last5, na.rm=TRUE),
# last10=mean(last10, na.rm=TRUE),
# last20=mean(last20, na.rm=TRUE),
# last50=mean(last50, na.rm=TRUE)
# )
#
# # fill in averages
# na.merge = merge(all2, na.avg, by=c("weekend","hour"))
# na.merge = na.merge[order(na.merge$id),]
# for(i in c("last1", "last3", "last5", "last10", "last20", "last50")) {
# y = paste0(i, ".y")
# idx = is.na(all2[[i]])
# all2[idx,][[i]] <- na.merge[idx,][[y]]
# }
# rm(na.avg, na.merge, b, i, idx, n, pd, sec, sh, y, z)
}
}
rm(last1, last10, last100)## Warning in rm(last1, last10, last100): object 'last1' not found## Warning in rm(last1, last10, last100): object 'last10' not found## Warning in rm(last1, last10, last100): object 'last100' not found# Create factors of string variables
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "factorize.str.vars"), major.inc=TRUE)## label step_major step_minor bgn end
## 1 extract.features_bgn 1 0 16.455 16.468
## 2 extract.features_factorize.str.vars 2 0 16.469 NA
## elapsed
## 1 0.013
## 2 NA#stop(here"); sav_allobs_df <- glb_allobs_df; #glb_allobs_df <- sav_allobs_df
print(str_vars <- myfind_chr_cols_df(glb_allobs_df))## description condition cellular carrier color
## "description" "condition" "cellular" "carrier" "color"
## storage productline .src prdline.my
## "storage" "productline" ".src" "prdline.my"if (length(str_vars <- setdiff(str_vars,
c(glb_exclude_vars_as_features, glb_txt_vars))) > 0) {
for (var in str_vars) {
warning("Creating factors of string variable: ", var,
": # of unique values: ", length(unique(glb_allobs_df[, var])))
glb_allobs_df[, paste0(var, ".fctr")] <-
relevel(factor(glb_allobs_df[, var]),
names(which.max(table(glb_allobs_df[, var], useNA = "ifany"))))
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, str_vars)
}## Warning: Creating factors of string variable: condition: # of unique
## values: 6## Warning: Creating factors of string variable: cellular: # of unique values:
## 3## Warning: Creating factors of string variable: carrier: # of unique values:
## 7## Warning: Creating factors of string variable: color: # of unique values: 5## Warning: Creating factors of string variable: storage: # of unique values:
## 5## Warning: Creating factors of string variable: prdline.my: # of unique
## values: 12if (!is.null(glb_txt_vars)) {
require(foreach)
require(gsubfn)
require(stringr)
require(tm)
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "process.text"), major.inc=TRUE)
chk_pattern_freq <- function(rex_str, ignore.case=TRUE) {
match_mtrx <- str_extract_all(txt_vctr, regex(rex_str, ignore_case=ignore.case),
simplify=TRUE)
match_df <- as.data.frame(match_mtrx[match_mtrx != ""])
names(match_df) <- "pattern"
return(mycreate_sqlxtab_df(match_df, "pattern"))
}
# match_lst <- gregexpr("\\bok(?!ay)", txt_vctr[746], ignore.case = FALSE, perl=TRUE); print(match_lst)
dsp_pattern <- function(rex_str, ignore.case=TRUE, print.all=TRUE) {
match_lst <- gregexpr(rex_str, txt_vctr, ignore.case = ignore.case, perl=TRUE)
match_lst <- regmatches(txt_vctr, match_lst)
match_df <- data.frame(matches=sapply(match_lst,
function (elems) paste(elems, collapse="#")))
match_df <- subset(match_df, matches != "")
if (print.all)
print(match_df)
return(match_df)
}
dsp_matches <- function(rex_str, ix) {
print(match_pos <- gregexpr(rex_str, txt_vctr[ix], perl=TRUE))
print(str_sub(txt_vctr[ix], (match_pos[[1]] / 100) * 99 + 0,
(match_pos[[1]] / 100) * 100 + 100))
}
myapply_gsub <- function(...) {
if ((length_lst <- length(names(gsub_map_lst))) == 0)
return(txt_vctr)
for (ptn_ix in 1:length_lst) {
if ((ptn_ix %% 10) == 0)
print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix,
length(names(gsub_map_lst)), names(gsub_map_lst)[ptn_ix]))
txt_vctr <- gsub(names(gsub_map_lst)[ptn_ix], gsub_map_lst[[ptn_ix]],
txt_vctr, ...)
}
return(txt_vctr)
}
myapply_txtmap <- function(txt_vctr, ...) {
nrows <- nrow(glb_txt_map_df)
for (ptn_ix in 1:nrows) {
if ((ptn_ix %% 10) == 0)
print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix,
nrows, glb_txt_map_df[ptn_ix, "rex_str"]))
txt_vctr <- gsub(glb_txt_map_df[ptn_ix, "rex_str"],
glb_txt_map_df[ptn_ix, "rpl_str"],
txt_vctr, ...)
}
return(txt_vctr)
}
chk.equal <- function(bgn, end) {
print(all.equal(sav_txt_lst[["Headline"]][bgn:end],
glb_txt_lst[["Headline"]][bgn:end]))
}
dsp.equal <- function(bgn, end) {
print(sav_txt_lst[["Headline"]][bgn:end])
print(glb_txt_lst[["Headline"]][bgn:end])
}
#sav_txt_lst <- glb_txt_lst; all.equal(sav_txt_lst, glb_txt_lst)
#all.equal(sav_txt_lst[["Headline"]][1:4200], glb_txt_lst[["Headline"]][1:4200])
#chk.equal( 1, 100)
#dsp.equal(86, 90)
txt_map_filename <- paste0(glb_txt_munge_filenames_pfx, "map.csv")
if (!file.exists(txt_map_filename))
stop(txt_map_filename, " not found!")
glb_txt_map_df <- read.csv(txt_map_filename, comment.char="#", strip.white=TRUE)
glb_txt_lst <- list();
print(sprintf("Building glb_txt_lst..."))
glb_txt_lst <- foreach(txt_var=glb_txt_vars) %dopar% {
# for (txt_var in glb_txt_vars) {
txt_vctr <- glb_allobs_df[, txt_var]
# myapply_txtmap shd be created as a tm_map::content_transformer ?
#print(glb_txt_map_df)
#txt_var=glb_txt_vars[3]; txt_vctr <- glb_txt_lst[[txt_var]]
#print(rex_str <- glb_txt_map_df[163, "rex_str"])
#print(rex_str <- glb_txt_map_df[glb_txt_map_df$rex_str == "\\bWall St\\.", "rex_str"])
#print(rex_str <- glb_txt_map_df[grepl("du Pont", glb_txt_map_df$rex_str), "rex_str"])
#print(rex_str <- glb_txt_map_df[glb_txt_map_df$rpl_str == "versus", "rex_str"])
#print(tmp_vctr <- grep(rex_str, txt_vctr, value=TRUE, ignore.case=FALSE))
#ret_lst <- regexec(rex_str, txt_vctr, ignore.case=FALSE); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])
#gsub(rex_str, glb_txt_map_df[glb_txt_map_df$rex_str == rex_str, "rpl_str"], tmp_vctr, ignore.case=FALSE)
#grep("Hong Hong", txt_vctr, value=TRUE)
txt_vctr <- myapply_txtmap(txt_vctr, ignore.case=FALSE)
}
names(glb_txt_lst) <- glb_txt_vars
for (txt_var in glb_txt_vars) {
print(sprintf("Remaining OK in %s:", txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(chk_pattern_freq(rex_str <- "(?<!(BO|HO|LO))OK(?!(E\\!|ED|IE|IN|S ))",
ignore.case=FALSE))
match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
for (row in row.names(match_df))
dsp_matches(rex_str, ix=as.numeric(row))
print(chk_pattern_freq(rex_str <- "Ok(?!(a\\.|ay|in|ra|um))", ignore.case=FALSE))
match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
for (row in row.names(match_df))
dsp_matches(rex_str, ix=as.numeric(row))
print(chk_pattern_freq(rex_str <- "(?<!( b| B| c| C| g| G| j| M| p| P| w| W| r| Z|\\(b|ar|bo|Bo|co|Co|Ew|gk|go|ho|ig|jo|kb|ke|Ke|ki|lo|Lo|mo|mt|no|No|po|ra|ro|sm|Sm|Sp|to|To))ok(?!(ay|bo|e |e\\)|e,|e\\.|eb|ed|el|en|er|es|ey|i |ie|in|it|ka|ke|ki|ly|on|oy|ra|st|u |uc|uy|yl|yo))",
ignore.case=FALSE))
match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
for (row in row.names(match_df))
dsp_matches(rex_str, ix=as.numeric(row))
}
# txt_vctr <- glb_txt_lst[[glb_txt_vars[1]]]
# print(chk_pattern_freq(rex_str <- "(?<!( b| c| C| p|\\(b|bo|co|lo|Lo|Sp|to|To))ok(?!(ay|e |e\\)|e,|e\\.|ed|el|en|es|ey|ie|in|on|ra))", ignore.case=FALSE))
# print(chk_pattern_freq(rex_str <- "ok(?!(ay|el|on|ra))", ignore.case=FALSE))
# dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
# dsp_matches(rex_str, ix=8)
# substr(txt_vctr[86], 5613, 5620)
# substr(glb_allobs_df[301, "review"], 550, 650)
#stop(here"); sav_txt_lst <- glb_txt_lst
for (txt_var in glb_txt_vars) {
print(sprintf("Remaining Acronyms in %s:", txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(chk_pattern_freq(rex_str <- "([[:upper:]]\\.( *)){2,}", ignore.case=FALSE))
# Check for names
print(subset(chk_pattern_freq(rex_str <- "(([[:upper:]]+)\\.( *)){1}",
ignore.case=FALSE),
.n > 1))
# dsp_pattern(rex_str="(OK\\.( *)){1}", ignore.case=FALSE)
# dsp_matches(rex_str="(OK\\.( *)){1}", ix=557)
#dsp_matches(rex_str="\\bR\\.I\\.P(\\.*)(\\B)", ix=461)
#dsp_matches(rex_str="\\bR\\.I\\.P(\\.*)", ix=461)
#print(str_sub(txt_vctr[676], 10100, 10200))
#print(str_sub(txt_vctr[74], 1, -1))
}
for (txt_var in glb_txt_vars) {
re_str <- "\\b(Fort|Ft\\.|Hong|Las|Los|New|Puerto|Saint|San|St\\.)( |-)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl("( |-)[[:upper:]]", pattern))))
print(" consider cleaning if relevant to problem domain; geography name; .n > 1")
#grep("New G", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("St\\. Wins", txt_vctr, value=TRUE, ignore.case=FALSE)
}
#stop(here"); sav_txt_lst <- glb_txt_lst
for (txt_var in glb_txt_vars) {
re_str <- "\\b(N|S|E|W|C)( |\\.)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl(".", pattern))))
#grep("N Weaver", txt_vctr, value=TRUE, ignore.case=FALSE)
}
for (txt_var in glb_txt_vars) {
re_str <- "\\b(North|South|East|West|Central)( |\\.)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
if (nrow(filtered_df <- subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl(".", pattern))) > 0)
print(orderBy(~ -.n +pattern, filtered_df))
#grep("Central (African|Bankers|Cast|Italy|Role|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("East (Africa|Berlin|London|Poland|Rivals|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("North (American|Korean|West)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("South (Pacific|Street)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("St\\. Martins", txt_vctr, value=TRUE, ignore.case=FALSE)
}
find_cmpnd_wrds <- function(txt_vctr) {
txt_corpus <- Corpus(VectorSource(txt_vctr))
txt_corpus <- tm_map(txt_corpus, content_transformer(tolower), lazy=TRUE)
txt_corpus <- tm_map(txt_corpus, PlainTextDocument, lazy=TRUE)
txt_corpus <- tm_map(txt_corpus, removePunctuation, lazy=TRUE,
preserve_intra_word_dashes=TRUE, lazy=TRUE)
full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTf))
print(" Full TermMatrix:"); print(full_Tf_DTM)
full_Tf_mtrx <- as.matrix(full_Tf_DTM)
rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_Tf_vctr <- colSums(full_Tf_mtrx)
names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
#grep("year", names(full_Tf_vctr), value=TRUE)
#which.max(full_Tf_mtrx[, "yearlong"])
full_Tf_df <- as.data.frame(full_Tf_vctr)
names(full_Tf_df) <- "Tf.full"
full_Tf_df$term <- rownames(full_Tf_df)
#full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
full_Tf_df <- orderBy(~ -Tf.full, full_Tf_df)
cmpnd_Tf_df <- full_Tf_df[grep("-", full_Tf_df$term, value=TRUE) ,]
txt_compound_filename <- paste0(glb_txt_munge_filenames_pfx, "compound.csv")
if (!file.exists(txt_compound_filename))
stop(txt_compound_filename, " not found!")
filter_df <- read.csv(txt_compound_filename, comment.char="#", strip.white=TRUE)
cmpnd_Tf_df$filter <- FALSE
for (row_ix in 1:nrow(filter_df))
cmpnd_Tf_df[!cmpnd_Tf_df$filter, "filter"] <-
grepl(filter_df[row_ix, "rex_str"],
cmpnd_Tf_df[!cmpnd_Tf_df$filter, "term"], ignore.case=TRUE)
cmpnd_Tf_df <- subset(cmpnd_Tf_df, !filter)
# Bug in tm_map(txt_corpus, removePunctuation, preserve_intra_word_dashes=TRUE) ???
# "net-a-porter" gets converted to "net-aporter"
#grep("net-a-porter", txt_vctr, ignore.case=TRUE, value=TRUE)
#grep("maser-laser", txt_vctr, ignore.case=TRUE, value=TRUE)
#txt_corpus[[which(grepl("net-a-porter", txt_vctr, ignore.case=TRUE))]]
#grep("\\b(across|longer)-(\\w)", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
#grep("(\\w)-(affected|term)\\b", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
print(sprintf("nrow(cmpnd_Tf_df): %d", nrow(cmpnd_Tf_df)))
myprint_df(cmpnd_Tf_df)
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "process.text_reporting_compound_terms"), major.inc=FALSE)
for (txt_var in glb_txt_vars) {
print(sprintf("Remaining compound terms in %s: ", txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
# find_cmpnd_wrds(txt_vctr)
#grep("thirty-five", txt_vctr, ignore.case=TRUE, value=TRUE)
#rex_str <- glb_txt_map_df[grepl("hirty", glb_txt_map_df$rex_str), "rex_str"]
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "build.corpus"), major.inc=TRUE)
glb_corpus_lst <- list()
print(sprintf("Building glb_corpus_lst..."))
glb_corpus_lst <- foreach(txt_var=glb_txt_vars) %dopar% {
# for (txt_var in glb_txt_vars) {
txt_corpus <- Corpus(VectorSource(glb_txt_lst[[txt_var]]))
txt_corpus <- tm_map(txt_corpus, content_transformer(tolower), lazy=TRUE) #nuppr
txt_corpus <- tm_map(txt_corpus, PlainTextDocument, lazy=TRUE)
txt_corpus <- tm_map(txt_corpus, removePunctuation, lazy=TRUE) #npnct<chr_ix>
# txt-corpus <- tm_map(txt_corpus, content_transformer(function(x, pattern) gsub(pattern, "", x))
# Not to be run in production
inspect_terms <- function() {
full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTf))
print(" Full TermMatrix:"); print(full_Tf_DTM)
full_Tf_mtrx <- as.matrix(full_Tf_DTM)
rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_Tf_vctr <- colSums(full_Tf_mtrx)
names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
#grep("year", names(full_Tf_vctr), value=TRUE)
#which.max(full_Tf_mtrx[, "yearlong"])
full_Tf_df <- as.data.frame(full_Tf_vctr)
names(full_Tf_df) <- "Tf.full"
full_Tf_df$term <- rownames(full_Tf_df)
#full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
full_Tf_df <- orderBy(~ -Tf.full +term, full_Tf_df)
print(myplot_histogram(full_Tf_df, "Tf.full"))
myprint_df(full_Tf_df)
#txt_corpus[[which(grepl("zun", txt_vctr, ignore.case=TRUE))]]
digit_terms_df <- subset(full_Tf_df, grepl("[[:digit:]]", term))
myprint_df(digit_terms_df)
return(full_Tf_df)
}
#print("RemovePunct:"); remove_punct_Tf_df <- inspect_terms()
txt_corpus <- tm_map(txt_corpus, removeWords,
c(glb_append_stop_words[[txt_var]],
stopwords("english")), lazy=TRUE) #nstopwrds
#print("StoppedWords:"); stopped_words_Tf_df <- inspect_terms()
txt_corpus <- tm_map(txt_corpus, stemDocument, lazy=TRUE) #Features for lost information: Difference/ratio in density of full_TfIdf_DTM ???
#txt_corpus <- tm_map(txt_corpus, content_transformer(stemDocument))
#print("StemmedWords:"); stemmed_words_Tf_df <- inspect_terms()
#stemmed_stopped_Tf_df <- merge(stemmed_words_Tf_df, stopped_words_Tf_df, by="term", all=TRUE, suffixes=c(".stem", ".stop"))
#myprint_df(stemmed_stopped_Tf_df)
#print(subset(stemmed_stopped_Tf_df, grepl("compan", term)))
#glb_corpus_lst[[txt_var]] <- txt_corpus
}
names(glb_corpus_lst) <- glb_txt_vars
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "extract.DTM"), major.inc=TRUE)
glb_full_DTM_lst <- list(); glb_sprs_DTM_lst <- list();
for (txt_var in glb_txt_vars) {
print(sprintf("Extracting TfIDf terms for %s...", txt_var))
txt_corpus <- glb_corpus_lst[[txt_var]]
# full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
# control=list(weighting=weightTf))
full_TfIdf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTfIdf))
sprs_TfIdf_DTM <- removeSparseTerms(full_TfIdf_DTM,
glb_sprs_thresholds[txt_var])
# glb_full_DTM_lst[[txt_var]] <- full_Tf_DTM
# glb_sprs_DTM_lst[[txt_var]] <- sprs_Tf_DTM
glb_full_DTM_lst[[txt_var]] <- full_TfIdf_DTM
glb_sprs_DTM_lst[[txt_var]] <- sprs_TfIdf_DTM
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "report.DTM"), major.inc=TRUE)
for (txt_var in glb_txt_vars) {
print(sprintf("Reporting TfIDf terms for %s...", txt_var))
full_TfIdf_DTM <- glb_full_DTM_lst[[txt_var]]
sprs_TfIdf_DTM <- glb_sprs_DTM_lst[[txt_var]]
print(" Full TermMatrix:"); print(full_TfIdf_DTM)
full_TfIdf_mtrx <- as.matrix(full_TfIdf_DTM)
rownames(full_TfIdf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_TfIdf_vctr <- colSums(full_TfIdf_mtrx)
names(full_TfIdf_vctr) <- dimnames(full_TfIdf_DTM)[[2]]
#grep("scene", names(full_TfIdf_vctr), value=TRUE)
#which.max(full_TfIdf_mtrx[, "yearlong"])
full_TfIdf_df <- as.data.frame(full_TfIdf_vctr)
names(full_TfIdf_df) <- "TfIdf.full"
full_TfIdf_df$term <- rownames(full_TfIdf_df)
full_TfIdf_df$freq.full <- colSums(full_TfIdf_mtrx != 0)
full_TfIdf_df <- orderBy(~ -TfIdf.full, full_TfIdf_df)
print(" Sparse TermMatrix:"); print(sprs_TfIdf_DTM)
sprs_TfIdf_vctr <- colSums(as.matrix(sprs_TfIdf_DTM))
names(sprs_TfIdf_vctr) <- dimnames(sprs_TfIdf_DTM)[[2]]
sprs_TfIdf_df <- as.data.frame(sprs_TfIdf_vctr)
names(sprs_TfIdf_df) <- "TfIdf.sprs"
sprs_TfIdf_df$term <- rownames(sprs_TfIdf_df)
sprs_TfIdf_df$freq.sprs <- colSums(as.matrix(sprs_TfIdf_DTM) != 0)
sprs_TfIdf_df <- orderBy(~ -TfIdf.sprs, sprs_TfIdf_df)
terms_TfIdf_df <- merge(full_TfIdf_df, sprs_TfIdf_df, all.x=TRUE)
terms_TfIdf_df$in.sprs <- !is.na(terms_TfIdf_df$freq.sprs)
plt_TfIdf_df <- subset(terms_TfIdf_df,
TfIdf.full >= min(terms_TfIdf_df$TfIdf.sprs, na.rm=TRUE))
plt_TfIdf_df$label <- ""
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "label"] <-
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"]
glb_important_terms[[txt_var]] <- union(glb_important_terms[[txt_var]],
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"])
print(myplot_scatter(plt_TfIdf_df, "freq.full", "TfIdf.full",
colorcol_name="in.sprs") +
geom_text(aes(label=label), color="Black", size=3.5))
melt_TfIdf_df <- orderBy(~ -value, melt(terms_TfIdf_df, id.var="term"))
print(ggplot(melt_TfIdf_df, aes(value, color=variable)) + stat_ecdf() +
geom_hline(yintercept=glb_sprs_thresholds[txt_var],
linetype = "dotted"))
melt_TfIdf_df <- orderBy(~ -value,
melt(subset(terms_TfIdf_df, !is.na(TfIdf.sprs)), id.var="term"))
print(myplot_hbar(melt_TfIdf_df, "term", "value",
colorcol_name="variable"))
melt_TfIdf_df <- orderBy(~ -value,
melt(subset(terms_TfIdf_df, is.na(TfIdf.sprs)), id.var="term"))
print(myplot_hbar(head(melt_TfIdf_df, 10), "term", "value",
colorcol_name="variable"))
}
# sav_full_DTM_lst <- glb_full_DTM_lst
# sav_sprs_DTM_lst <- glb_sprs_DTM_lst
# print(identical(sav_glb_corpus_lst, glb_corpus_lst))
# print(all.equal(length(sav_glb_corpus_lst), length(glb_corpus_lst)))
# print(all.equal(names(sav_glb_corpus_lst), names(glb_corpus_lst)))
# print(all.equal(sav_glb_corpus_lst[["Headline"]], glb_corpus_lst[["Headline"]]))
# print(identical(sav_full_DTM_lst, glb_full_DTM_lst))
# print(identical(sav_sprs_DTM_lst, glb_sprs_DTM_lst))
rm(full_TfIdf_mtrx, full_TfIdf_df, melt_TfIdf_df, terms_TfIdf_df)
# Create txt features
if ((length(glb_txt_vars) > 1) &&
(length(unique(pfxs <- sapply(glb_txt_vars,
function(txt) toupper(substr(txt, 1, 1))))) < length(glb_txt_vars)))
stop("Prefixes for corpus freq terms not unique: ", pfxs)
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "bind.DTM"),
major.inc=TRUE)
for (txt_var in glb_txt_vars) {
print(sprintf("Binding DTM for %s...", txt_var))
txt_var_pfx <- toupper(substr(txt_var, 1, 1))
txt_X_df <- as.data.frame(as.matrix(glb_sprs_DTM_lst[[txt_var]]))
colnames(txt_X_df) <- paste(txt_var_pfx, ".T.",
make.names(colnames(txt_X_df)), sep="")
rownames(txt_X_df) <- rownames(glb_allobs_df) # warning otherwise
# plt_X_df <- cbind(txt_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
# print(myplot_box(df=plt_X_df, ycol_names="H.T.today", xcol_name=glb_rsp_var))
# log_X_df <- log(1 + txt_X_df)
# colnames(log_X_df) <- paste(colnames(txt_X_df), ".log", sep="")
# plt_X_df <- cbind(log_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
# print(myplot_box(df=plt_X_df, ycol_names="H.T.today.log", xcol_name=glb_rsp_var))
glb_allobs_df <- cbind(glb_allobs_df, txt_X_df) # TfIdf is normalized
#glb_allobs_df <- cbind(glb_allobs_df, log_X_df) # if using non-normalized metrics
}
#identical(chk_entity_df, glb_allobs_df)
#chk_entity_df <- glb_allobs_df
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "bind.DXM"),
major.inc=TRUE)
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
glb_punct_vctr <- c("!", "\"", "#", "\\$", "%", "&", "'",
"\\(|\\)",# "\\(", "\\)",
"\\*", "\\+", ",", "-", "\\.", "/", ":", ";",
"<|>", # "<",
"=",
# ">",
"\\?", "@", "\\[", "\\\\", "\\]", "^", "_", "`",
"\\{", "\\|", "\\}", "~")
txt_X_df <- glb_allobs_df[, c(glb_id_var, ".rnorm"), FALSE]
txt_X_df <- foreach(txt_var=glb_txt_vars, .combine=cbind) %dopar% {
#for (txt_var in glb_txt_vars) {
print(sprintf("Binding DXM for %s...", txt_var))
txt_var_pfx <- toupper(substr(txt_var, 1, 1))
txt_full_DTM_mtrx <- as.matrix(glb_full_DTM_lst[[txt_var]])
rownames(txt_full_DTM_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
#print(txt_full_DTM_mtrx[txt_full_DTM_mtrx[, "ebola"] != 0, "ebola"])
# Create <txt_var>.T.<term> for glb_important_terms
for (term in glb_important_terms[[txt_var]])
txt_X_df[, paste0(txt_var_pfx, ".T.", make.names(term))] <-
txt_full_DTM_mtrx[, term]
# Create <txt_var>.nwrds.log & .nwrds.unq.log
txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")] <-
log(1 + mycount_pattern_occ("\\w+", glb_txt_lst[[txt_var]]))
txt_X_df[, paste0(txt_var_pfx, ".nwrds.unq.log")] <-
log(1 + rowSums(txt_full_DTM_mtrx != 0))
txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] <-
rowSums(txt_full_DTM_mtrx)
txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <-
txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] /
(exp(txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")]) - 1)
txt_X_df[is.nan(txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")]),
paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <- 0
# Create <txt_var>.nchrs.log
txt_X_df[, paste0(txt_var_pfx, ".nchrs.log")] <-
log(1 + mycount_pattern_occ(".", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".nuppr.log")] <-
log(1 + mycount_pattern_occ("[[:upper:]]", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".ndgts.log")] <-
log(1 + mycount_pattern_occ("[[:digit:]]", glb_allobs_df[, txt_var]))
# Create <txt_var>.npnct?.log
# would this be faster if it's iterated over each row instead of
# each created column ???
for (punct_ix in 1:length(glb_punct_vctr)) {
# smp0 <- " "
# smp1 <- "! \" # $ % & ' ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ ` { | } ~"
# smp2 <- paste(smp1, smp1, sep=" ")
# print(sprintf("Testing %s pattern:", glb_punct_vctr[punct_ix]))
# results <- mycount_pattern_occ(glb_punct_vctr[punct_ix], c(smp0, smp1, smp2))
# names(results) <- NULL; print(results)
txt_X_df[,
paste0(txt_var_pfx, ".npnct", sprintf("%02d", punct_ix), ".log")] <-
log(1 + mycount_pattern_occ(glb_punct_vctr[punct_ix],
glb_allobs_df[, txt_var]))
}
# print(head(glb_allobs_df[glb_allobs_df[, "A.npnct23.log"] > 0,
# c("UniqueID", "Popular", "Abstract", "A.npnct23.log")]))
# Create <txt_var>.nstopwrds.log & <txt_var>ratio.nstopwrds.nwrds
stop_words_rex_str <- paste0("\\b(", paste0(c(glb_append_stop_words[[txt_var]],
stopwords("english")), collapse="|"),
")\\b")
txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] <-
log(1 + mycount_pattern_occ(stop_words_rex_str, glb_txt_lst[[txt_var]]))
txt_X_df[, paste0(txt_var_pfx, ".ratio.nstopwrds.nwrds")] <-
exp(txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] -
txt_X_df[, paste0(txt_var_pfx, ".nwrds", ".log")])
# Create <txt_var>.P.http
txt_X_df[, paste(txt_var_pfx, ".P.http", sep="")] <-
as.integer(0 + mycount_pattern_occ("http", glb_allobs_df[, txt_var]))
# Create <txt_var>.P.mini & air
txt_X_df[, paste(txt_var_pfx, ".P.mini", sep="")] <-
as.integer(0 + mycount_pattern_occ("mini(?!m)", glb_allobs_df[, txt_var],
perl=TRUE))
txt_X_df[, paste(txt_var_pfx, ".P.air", sep="")] <-
as.integer(0 + mycount_pattern_occ("(?<![fhp])air", glb_allobs_df[, txt_var],
perl=TRUE))
txt_X_df <- subset(txt_X_df, select=-.rnorm)
txt_X_df <- txt_X_df[, -grep(glb_id_var, names(txt_X_df), fixed=TRUE), FALSE]
#glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
}
glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
#myplot_box(glb_allobs_df, "A.sum.TfIdf", glb_rsp_var)
# if (sum(is.na(glb_allobs_df$D.P.http)) > 0)
# stop("Why is this happening ?")
# Generate summaries
# print(summary(glb_allobs_df))
# print(sapply(names(glb_allobs_df), function(col) sum(is.na(glb_allobs_df[, col]))))
# print(summary(glb_trnobs_df))
# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(summary(glb_newobs_df))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
glb_txt_vars)
rm(log_X_df, txt_X_df)
}## Loading required package: stringr
## Loading required package: tm
## Loading required package: NLP
##
## Attaching package: 'NLP'
##
## The following object is masked from 'package:ggplot2':
##
## annotate## label step_major step_minor bgn end
## 2 extract.features_factorize.str.vars 2 0 16.469 16.833
## 3 extract.features_process.text 3 0 16.834 NA
## elapsed
## 2 0.365
## 3 NA
## [1] "Building glb_txt_lst..."
## [1] "running gsub for 10 (of 171): #\\bA\\.D\\.P\\.#..."
## [1] "running gsub for 20 (of 171): #\\bA\\.P\\.#..."
## [1] "running gsub for 30 (of 171): #\\bC\\.I\\.C\\.C\\.#..."
## [1] "running gsub for 40 (of 171): #\\bE\\.J\\. Manuel#..."
## [1] "running gsub for 50 (of 171): #\\bF\\.T\\.C\\.#..."
## [1] "running gsub for 60 (of 171): #\\bI\\.M\\.F\\.#..."
## [1] "running gsub for 70 (of 171): #\\bJ\\.F\\.K\\.#..."
## [1] "running gsub for 80 (of 171): #\\bM\\.&A\\.#..."
## [1] "running gsub for 90 (of 171): #\\bN\\.R\\.A\\.#..."
## [1] "running gsub for 100 (of 171): #\\bP\\.R\\.#..."
## [1] "running gsub for 110 (of 171): #\\bS\\.E\\.O\\.#..."
## [1] "running gsub for 120 (of 171): #\\bU\\.S\\.(A\\.)*#..."
## [1] "running gsub for 130 (of 171): #\\bW\\.M\\.D\\.#..."
## [1] "running gsub for 140 (of 171): #\\bLos( |-)((Angeles|Angeless)\\b)+#..."
## [1] "running gsub for 150 (of 171): #(\\w)-(Shanghai|USA)\\b#..."
## [1] "running gsub for 160 (of 171): #(one|two|three|four|five|six|seven|eight|nine)-#..."
## [1] "running gsub for 170 (of 171): #\\b[Ss]eventy-[Oo]ne\\b#..."
## [1] "Remaining OK in description:"
## pattern .n
## 1 OK 7
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN: Device has at least one or more problems: \nFor Parts or Repair"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN DEVICE: Problem with Apple ID"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN: Device has at least one or more problems: \nFor Parts or Repair"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN: Device has at least one or more problems: \nFor Parts or Repair"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN: Device has at least one or more problems: \nFor Parts or Repair"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN: Device has at least one or more problems: \nFor Parts or Repair"
## [[1]]
## [1] 3
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUE
## attr(,"capture.start")
##
## [1,] 0 0
## attr(,"capture.length")
##
## [1,] 0 0
## attr(,"capture.names")
## [1] "" ""
##
## [1] "ROKEN SCREEN"
## [1] pattern .n
## <0 rows> (or 0-length row.names)
## [1] pattern .n
## <0 rows> (or 0-length row.names)
## [1] "Remaining Acronyms in description:"
## [1] pattern .n
## <0 rows> (or 0-length row.names)
## pattern .n
## 1 ONLY. 7
## 2 CONDITION. 6
## 3 GB. 4
## 4 BOX. 2
## 5 CONDITION. 2
## 6 CORNER. 2
## 7 ESN. 2
## 8 GOOD. 2
## 9 ICLOUD. 2
## 10 IMEI. 2
## 11 IPADS. 2
## 12 LOCKED. 2
## 13 LOCKS. 2
## 14 ON. 2
## 15 SCRATCHES. 2
## 16 TEARS. 2
## 17 USE. 2
## [1] "Remaining #\\b(Fort|Ft\\.|Hong|Las|Los|New|Puerto|Saint|San|St\\.)( |-)(\\w)+# terms in description: "
## pattern .n
## 2 New Open 3
## 4 New Condition 2
## 7 New Digitizer 1
## 8 New Opened 1
## 9 New Scratch 1
## 10 New Screen 1
## 14 New-Other 1
## [1] " consider cleaning if relevant to problem domain; geography name; .n > 1"
## [1] "Remaining #\\b(N|S|E|W|C)( |\\.)(\\w)+# terms in description: "
## pattern .n
## 1 C Stock 3
## 2 W blue 1
## [1] "Remaining #\\b(North|South|East|West|Central)( |\\.)(\\w)+# terms in description: "
## label step_major
## 3 extract.features_process.text 3
## 4 extract.features_process.text_reporting_compound_terms 3
## step_minor bgn end elapsed
## 3 0 16.834 19.188 2.354
## 4 1 19.188 NA NA
## [1] "Remaining compound terms in description: "
## label step_major
## 4 extract.features_process.text_reporting_compound_terms 3
## 5 extract.features_build.corpus 4
## step_minor bgn end elapsed
## 4 1 19.188 19.192 0.005
## 5 0 19.193 NA NA
## [1] "Building glb_corpus_lst..."
## label step_major step_minor bgn end
## 5 extract.features_build.corpus 4 0 19.193 19.779
## 6 extract.features_extract.DTM 5 0 19.780 NA
## elapsed
## 5 0.587
## 6 NA
## [1] "Extracting TfIDf terms for description..."## Warning in weighting(x): empty document(s): character(0) character(0)
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## character(0) charact## label step_major step_minor bgn end elapsed
## 6 extract.features_extract.DTM 5 0 19.780 23.183 3.403
## 7 extract.features_report.DTM 6 0 23.183 NA NA
## [1] "Reporting TfIDf terms for description..."
## [1] " Full TermMatrix:"
## <<DocumentTermMatrix (documents: 2659, terms: 1123)>>
## Non-/sparse entries: 9175/2976882
## Sparsity : 100%
## Maximal term length: 27
## Weighting : term frequency - inverse document frequency (normalized) (tf-idf)
## [1] " Sparse TermMatrix:"
## <<DocumentTermMatrix (documents: 2659, terms: 10)>>
## Non-/sparse entries: 1989/24601
## Sparsity : 93%
## Maximal term length: 9
## Weighting : term frequency - inverse document frequency (normalized) (tf-idf)## Warning in myplot_scatter(plt_TfIdf_df, "freq.full", "TfIdf.full",
## colorcol_name = "in.sprs"): converting in.sprs to class:factor
## Warning: Removed 6 rows containing missing values (geom_path).## Warning: Removed 6 rows containing missing values (geom_path).
## label step_major step_minor bgn end elapsed
## 7 extract.features_report.DTM 6 0 23.183 25.694 2.511
## 8 extract.features_bind.DTM 7 0 25.695 NA NA
## [1] "Binding DTM for description..."
## label step_major step_minor bgn end elapsed
## 8 extract.features_bind.DTM 7 0 25.695 25.703 0.008
## 9 extract.features_bind.DXM 8 0 25.703 NA NA
## [1] "Binding DXM for description..."## Warning in rm(log_X_df, txt_X_df): object 'log_X_df' not found
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
# dsp_obs(list(description.contains="mini(?!m)"), perl=TRUE, cols="D.P.mini", all=TRUE)
# dsp_obs(list(D.P.mini=1), cols="D.P.mini", all=TRUE)
# dsp_obs(list(D.P.mini=1, productline="Unknown"), cols="D.P.mini", all=TRUE)
# dsp_obs(list(description.contains="(?<![fhp])air"), perl=TRUE, all=TRUE)
# dsp_obs(list(description.contains="air"), perl=FALSE, cols="D.P.air", all=TRUE)
# dsp_obs(list(D.P.air=1, productline="Unknown"), cols="D.P.air", all=TRUE)
glb_allobs_df[(glb_allobs_df$D.P.mini == 1) & (glb_allobs_df$productline == "Unknown"), "prdline.my"] <- "iPad mini"
print(mycreate_sqlxtab_df(glb_allobs_df, c("prdline.my", "productline", "D.P.mini", glb_rsp_var)))## prdline.my productline D.P.mini sold.fctr .n
## 1 iPad 2 iPad 2 0 <NA> 154
## 2 iPad 2 iPad 2 0 Y 147
## 3 iPad 2 iPad 2 0 N 139
## 4 iPad mini iPad mini 0 N 138
## 5 iPad mini iPad mini 0 Y 126
## 6 iPad 1 iPad 1 0 Y 125
## 7 Unknown Unknown 0 N 121
## 8 iPad mini iPad mini 0 <NA> 108
## 9 iPad 1 iPad 1 0 N 102
## 10 iPad Air iPad Air 0 N 102
## 11 iPad Air 2 iPad Air 2 0 N 100
## 12 iPad 4 iPad 4 0 N 93
## 13 Unknown Unknown 0 <NA> 89
## 14 iPad 1 iPad 1 0 <NA> 88
## 15 Unknown Unknown 0 Y 81
## 16 iPad 3 iPad 3 0 Y 80
## 17 iPad Air iPad Air 0 Y 78
## 18 iPad Air iPad Air 0 <NA> 74
## 19 iPad 3 iPad 3 0 N 73
## 20 iPad Air 2 iPad Air 2 0 Y 71
## 21 iPad 4 iPad 4 0 <NA> 68
## 22 iPad 4 iPad 4 0 Y 64
## 23 iPad Air 2 iPad Air 2 0 <NA> 62
## 24 iPad mini 3 iPad mini 3 0 N 61
## 25 iPad mini 2 iPad mini 2 0 N 56
## 26 iPad 3 iPad 3 0 <NA> 55
## 27 iPad mini 2 iPad mini 2 0 <NA> 52
## 28 iPad mini 2 iPad mini 2 0 Y 48
## 29 iPad mini 3 iPad mini 3 0 <NA> 35
## 30 iPad mini 3 iPad mini 3 0 Y 27
## 31 iPad mini iPad mini 1 N 7
## 32 iPad mini iPad mini 1 Y 5
## 33 iPad mini 2 iPad mini 2 1 <NA> 4
## 34 iPad mini Retina iPad mini Retina 0 Y 4
## 35 iPad mini Unknown 1 <NA> 3
## 36 iPad mini iPad mini 1 <NA> 3
## 37 iPad mini 3 iPad mini 3 1 <NA> 3
## 38 iPad mini Retina iPad mini Retina 0 N 3
## 39 iPad mini 2 iPad mini 2 1 N 2
## 40 iPad mini 3 iPad mini 3 1 N 2
## 41 iPad 5 iPad 5 0 Y 1
## 42 iPad mini Unknown 1 N 1
## 43 iPad mini Unknown 1 Y 1
## 44 iPad mini iPad mini 2 Y 1
## 45 iPad mini 2 iPad mini 2 1 Y 1
## 46 iPad mini Retina iPad mini Retina 1 N 1glb_allobs_df[glb_allobs_df$UniqueID == 11863, "D.P.air"] <- 0
glb_allobs_df[(glb_allobs_df$D.P.air == 1) & (glb_allobs_df$productline == "Unknown"), "prdline.my"] <- "iPad Air"
print(mycreate_sqlxtab_df(glb_allobs_df, c("prdline.my", "productline", "D.P.air", glb_rsp_var)))## prdline.my productline D.P.air sold.fctr .n
## 1 iPad 2 iPad 2 0 <NA> 154
## 2 iPad 2 iPad 2 0 Y 147
## 3 iPad mini iPad mini 0 N 145
## 4 iPad 2 iPad 2 0 N 139
## 5 iPad mini iPad mini 0 Y 132
## 6 iPad 1 iPad 1 0 Y 125
## 7 Unknown Unknown 0 N 120
## 8 iPad mini iPad mini 0 <NA> 111
## 9 iPad 1 iPad 1 0 N 102
## 10 iPad Air iPad Air 0 N 98
## 11 iPad Air 2 iPad Air 2 0 N 97
## 12 iPad 4 iPad 4 0 N 92
## 13 Unknown Unknown 0 <NA> 88
## 14 iPad 1 iPad 1 0 <NA> 88
## 15 Unknown Unknown 0 Y 80
## 16 iPad 3 iPad 3 0 Y 79
## 17 iPad Air iPad Air 0 Y 75
## 18 iPad 3 iPad 3 0 N 73
## 19 iPad Air iPad Air 0 <NA> 73
## 20 iPad Air 2 iPad Air 2 0 Y 69
## 21 iPad 4 iPad 4 0 <NA> 68
## 22 iPad 4 iPad 4 0 Y 64
## 23 iPad mini 3 iPad mini 3 0 N 63
## 24 iPad Air 2 iPad Air 2 0 <NA> 60
## 25 iPad mini 2 iPad mini 2 0 N 58
## 26 iPad mini 2 iPad mini 2 0 <NA> 56
## 27 iPad 3 iPad 3 0 <NA> 55
## 28 iPad mini 2 iPad mini 2 0 Y 49
## 29 iPad mini 3 iPad mini 3 0 <NA> 38
## 30 iPad mini 3 iPad mini 3 0 Y 27
## 31 iPad Air iPad Air 1 N 4
## 32 iPad mini Retina iPad mini Retina 0 N 4
## 33 iPad mini Retina iPad mini Retina 0 Y 4
## 34 iPad Air iPad Air 1 Y 3
## 35 iPad mini Unknown 0 <NA> 3
## 36 iPad Air 2 iPad Air 2 1 <NA> 2
## 37 iPad Air 2 iPad Air 2 1 N 2
## 38 iPad Air 2 iPad Air 2 1 Y 2
## 39 iPad 3 iPad 3 1 Y 1
## 40 iPad 4 iPad 4 1 N 1
## 41 iPad 5 iPad 5 0 Y 1
## 42 iPad Air Unknown 1 <NA> 1
## 43 iPad Air Unknown 1 N 1
## 44 iPad Air Unknown 1 Y 1
## 45 iPad Air iPad Air 1 <NA> 1
## 46 iPad Air 2 iPad Air 2 2 N 1
## 47 iPad mini Unknown 0 N 1
## 48 iPad mini Unknown 0 Y 1glb_allobs_df[glb_allobs_df$UniqueID == 12156, "prdline.my"] <- "iPad 1"
glb_allobs_df[glb_allobs_df$UniqueID == 11811, "prdline.my"] <- "iPad 2"
glb_allobs_df[glb_allobs_df$UniqueID == 11767, "prdline.my"] <- "iPad 2"
glb_allobs_df[glb_allobs_df$UniqueID == 11767, "storage"] <- "32"
# dsp_obs(list(prdline.my="Unknown"), all=TRUE)
glb_allobs_df$prdline.my.fctr <- as.factor(glb_allobs_df$prdline.my)
glb_allobs_df$storage.fctr <- as.factor(glb_allobs_df$storage)
# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
# print(myplot_scatter(glb_trnobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))
rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
glb_full_DTM_lst, glb_sprs_DTM_lst, txt_corpus, txt_vctr)## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'corpus_lst' not foundextract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, "extract.features_end",
major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 9 extract.features_bind.DXM 8 0 25.703 36.509 10.806
## 10 extract.features_end 9 0 36.510 NA NAmyplt_chunk(extract.features_chunk_df)## label step_major
## 9 extract.features_bind.DXM 8
## 6 extract.features_extract.DTM 5
## 7 extract.features_report.DTM 6
## 3 extract.features_process.text 3
## 5 extract.features_build.corpus 4
## 2 extract.features_factorize.str.vars 2
## 1 extract.features_bgn 1
## 8 extract.features_bind.DTM 7
## 4 extract.features_process.text_reporting_compound_terms 3
## step_minor bgn end elapsed duration
## 9 0 25.703 36.509 10.806 10.806
## 6 0 19.780 23.183 3.403 3.403
## 7 0 23.183 25.694 2.511 2.511
## 3 0 16.834 19.188 2.354 2.354
## 5 0 19.193 19.779 0.587 0.586
## 2 0 16.469 16.833 0.365 0.364
## 1 0 16.455 16.468 0.013 0.013
## 8 0 25.695 25.703 0.008 0.008
## 4 1 19.188 19.192 0.005 0.004
## [1] "Total Elapsed Time: 36.509 secs"
# if (glb_save_envir)
# save(glb_feats_df,
# glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
# file=paste0(glb_out_pfx, "extract_features_dsk.RData"))
# load(paste0(glb_out_pfx, "extract_features_dsk.RData"))
replay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"data.training.all","data.new")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
glb_chunks_df <- myadd_chunk(glb_chunks_df, "cluster.data", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 5 extract.features 3 0 16.448 37.899 21.451
## 6 cluster.data 4 0 37.900 NA NAStep 4.0: cluster data
glb_chunks_df <- myadd_chunk(glb_chunks_df, "manage.missing.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 6 cluster.data 4 0 37.900 38.828 0.928
## 7 manage.missing.data 4 1 38.829 NA NA# If mice crashes with error: Error in get(as.character(FUN), mode = "function", envir = envir) : object 'State' of mode 'function' was not found
# consider excluding 'State' as a feature
# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
# glb_trnobs_df <- na.omit(glb_trnobs_df)
# glb_newobs_df <- na.omit(glb_newobs_df)
# df[is.na(df)] <- 0
mycheck_problem_data(glb_allobs_df)## [1] "numeric data missing in : "
## sold sold.fctr
## 798 798
## [1] "numeric data w/ 0s in : "
## biddable sold cellular.fctr
## 1446 1001 1595
## D.T.condit D.T.condition D.T.good
## 2455 2385 2463
## D.T.ipad D.T.new D.T.scratch
## 2432 2520 2431
## D.T.screen D.T.this D.T.use
## 2453 2503 2474
## D.T.work D.T.box D.T.excellent
## 2485 2553 2602
## D.T.great D.T.like D.T.used
## 2539 2591 2540
## D.T.veri D.nwrds.log D.nwrds.unq.log
## 2567 1521 1529
## D.sum.TfIdf D.ratio.sum.TfIdf.nwrds D.nchrs.log
## 1529 1529 1521
## D.nuppr.log D.ndgts.log D.npnct01.log
## 1523 2428 2581
## D.npnct02.log D.npnct03.log D.npnct04.log
## 2659 2616 2659
## D.npnct05.log D.npnct06.log D.npnct07.log
## 2594 2556 2659
## D.npnct08.log D.npnct09.log D.npnct10.log
## 2583 2643 2650
## D.npnct11.log D.npnct12.log D.npnct13.log
## 2303 2539 1934
## D.npnct14.log D.npnct15.log D.npnct16.log
## 2584 2638 2548
## D.npnct17.log D.npnct18.log D.npnct19.log
## 2659 2658 2659
## D.npnct20.log D.npnct21.log D.npnct22.log
## 2659 2659 2659
## D.npnct23.log D.npnct24.log D.npnct25.log
## 2659 1521 2659
## D.npnct26.log D.npnct27.log D.npnct28.log
## 2659 2659 2651
## D.npnct29.log D.npnct30.log D.nstopwrds.log
## 2659 2659 1669
## D.P.http D.P.mini D.P.air
## 2659 2625 2639
## [1] "numeric data w/ Infs in : "
## named integer(0)
## [1] "numeric data w/ NaNs in : "
## named integer(0)
## [1] "string data missing in : "
## description condition cellular carrier color storage
## 1521 0 0 0 0 0
## productline prdline.my
## 0 0# glb_allobs_df <- na.omit(glb_allobs_df)
# Not refactored into mydsutils.R since glb_*_df might be reassigned
glb_impute_missing_data <- function() {
require(mice)
set.seed(glb_mice_complete.seed)
inp_impent_df <- glb_allobs_df[, setdiff(names(glb_allobs_df),
union(glb_exclude_vars_as_features, glb_rsp_var))]
print("Summary before imputation: ")
print(summary(inp_impent_df))
out_impent_df <- complete(mice(inp_impent_df))
print(summary(out_impent_df))
ret_vars <- sapply(names(out_impent_df),
function(col) ifelse(!identical(out_impent_df[, col],
inp_impent_df[, col]),
col, ""))
ret_vars <- ret_vars[ret_vars != ""]
# complete(mice()) changes attributes of factors even though values don't change
for (col in ret_vars) {
if (inherits(out_impent_df[, col], "factor")) {
if (identical(as.numeric(out_impent_df[, col]),
as.numeric(inp_impent_df[, col])))
ret_vars <- setdiff(ret_vars, col)
}
}
return(out_impent_df[, ret_vars])
}
if (glb_impute_na_data &&
(length(myfind_numerics_missing(glb_allobs_df)) > 0) &&
(ncol(nonna_df <- glb_impute_missing_data()) > 0)) {
for (col in names(nonna_df)) {
glb_allobs_df[, paste0(col, ".nonNA")] <- nonna_df[, col]
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, col)
}
}
mycheck_problem_data(glb_allobs_df, terminate = TRUE)## [1] "numeric data missing in : "
## sold sold.fctr
## 798 798
## [1] "numeric data w/ 0s in : "
## biddable sold cellular.fctr
## 1446 1001 1595
## D.T.condit D.T.condition D.T.good
## 2455 2385 2463
## D.T.ipad D.T.new D.T.scratch
## 2432 2520 2431
## D.T.screen D.T.this D.T.use
## 2453 2503 2474
## D.T.work D.T.box D.T.excellent
## 2485 2553 2602
## D.T.great D.T.like D.T.used
## 2539 2591 2540
## D.T.veri D.nwrds.log D.nwrds.unq.log
## 2567 1521 1529
## D.sum.TfIdf D.ratio.sum.TfIdf.nwrds D.nchrs.log
## 1529 1529 1521
## D.nuppr.log D.ndgts.log D.npnct01.log
## 1523 2428 2581
## D.npnct02.log D.npnct03.log D.npnct04.log
## 2659 2616 2659
## D.npnct05.log D.npnct06.log D.npnct07.log
## 2594 2556 2659
## D.npnct08.log D.npnct09.log D.npnct10.log
## 2583 2643 2650
## D.npnct11.log D.npnct12.log D.npnct13.log
## 2303 2539 1934
## D.npnct14.log D.npnct15.log D.npnct16.log
## 2584 2638 2548
## D.npnct17.log D.npnct18.log D.npnct19.log
## 2659 2658 2659
## D.npnct20.log D.npnct21.log D.npnct22.log
## 2659 2659 2659
## D.npnct23.log D.npnct24.log D.npnct25.log
## 2659 1521 2659
## D.npnct26.log D.npnct27.log D.npnct28.log
## 2659 2659 2651
## D.npnct29.log D.npnct30.log D.nstopwrds.log
## 2659 2659 1669
## D.P.http D.P.mini D.P.air
## 2659 2625 2639
## [1] "numeric data w/ Infs in : "
## named integer(0)
## [1] "numeric data w/ NaNs in : "
## named integer(0)
## [1] "string data missing in : "
## description condition cellular carrier color storage
## 1521 0 0 0 0 0
## productline prdline.my
## 0 0Step 4.1: manage missing data
if (glb_cluster) {
require(proxy)
#require(hash)
require(dynamicTreeCut)
# glb_hash <- hash(key=unique(glb_allobs_df$myCategory),
# values=1:length(unique(glb_allobs_df$myCategory)))
# glb_hash_lst <- hash(key=unique(glb_allobs_df$myCategory),
# values=1:length(unique(glb_allobs_df$myCategory)))
#stophere; sav_allobs_df <- glb_allobs_df;
print("Clustering features: ")
print(cluster_vars <- grep("[HSA]\\.[PT]\\.", names(glb_allobs_df), value=TRUE))
#print(cluster_vars <- grep("[HSA]\\.", names(glb_allobs_df), value=TRUE))
glb_allobs_df$.clusterid <- 1
#print(max(table(glb_allobs_df$myCategory.fctr) / 20))
for (myCategory in c("##", "Business#Business Day#Dealbook", "OpEd#Opinion#",
"Styles#U.S.#", "Business#Technology#", "Science#Health#",
"Culture#Arts#")) {
ctgry_allobs_df <- glb_allobs_df[glb_allobs_df$myCategory == myCategory, ]
dstns_dist <- dist(ctgry_allobs_df[, cluster_vars], method = "cosine")
dstns_mtrx <- as.matrix(dstns_dist)
print(sprintf("max distance(%0.4f) pair:", max(dstns_mtrx)))
row_ix <- ceiling(which.max(dstns_mtrx) / ncol(dstns_mtrx))
col_ix <- which.max(dstns_mtrx[row_ix, ])
print(ctgry_allobs_df[c(row_ix, col_ix),
c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])
min_dstns_mtrx <- dstns_mtrx
diag(min_dstns_mtrx) <- 1
print(sprintf("min distance(%0.4f) pair:", min(min_dstns_mtrx)))
row_ix <- ceiling(which.min(min_dstns_mtrx) / ncol(min_dstns_mtrx))
col_ix <- which.min(min_dstns_mtrx[row_ix, ])
print(ctgry_allobs_df[c(row_ix, col_ix),
c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])
clusters <- hclust(dstns_dist, method = "ward.D2")
#plot(clusters, labels=NULL, hang=-1)
myplclust(clusters, lab.col=unclass(ctgry_allobs_df[, glb_rsp_var]))
#clusterGroups = cutree(clusters, k=7)
clusterGroups <- cutreeDynamic(clusters, minClusterSize=20, method="tree", deepSplit=0)
# Unassigned groups are labeled 0; the largest group has label 1
table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
#print(ctgry_allobs_df[which(clusterGroups == 1), c("UniqueID", "Popular", "Headline")])
#print(ctgry_allobs_df[(clusterGroups == 1) & !is.na(ctgry_allobs_df$Popular) & (ctgry_allobs_df$Popular==1), c("UniqueID", "Popular", "Headline")])
clusterGroups[clusterGroups == 0] <- 1
table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
#summary(factor(clusterGroups))
# clusterGroups <- clusterGroups +
# 100 * # has to be > max(table(glb_allobs_df$myCategory.fctr) / minClusterSize=20)
# which(levels(glb_allobs_df$myCategory.fctr) == myCategory)
# table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
# add to glb_allobs_df - then split the data again
glb_allobs_df[glb_allobs_df$myCategory==myCategory,]$.clusterid <- clusterGroups
#print(unique(glb_allobs_df$.clusterid))
#print(glb_feats_df[glb_feats_df$id == ".clusterid.fctr", ])
}
ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
mycreate_sqlxtab_df(glb_allobs_df,
c("myCategory", ".clusterid", glb_rsp_var)))
ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df,
myCategory + .clusterid ~
Popular.fctr, sum, value.var=".n"))
print(ctgry_cast_df)
#print(orderBy(~ myCategory -Y -NA, ctgry_cast_df))
# write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_clst.csv"),
# row.names=FALSE)
print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df$.clusterid,
glb_allobs_df[, glb_rsp_var],
useNA="ifany"))
# dsp_obs(.clusterid=1, myCategory="OpEd#Opinion#",
# cols=c("UniqueID", "Popular", "myCategory", ".clusterid", "Headline"),
# all=TRUE)
glb_allobs_df$.clusterid.fctr <- as.factor(glb_allobs_df$.clusterid)
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features,
".clusterid")
glb_interaction_only_features["myCategory.fctr"] <- c(".clusterid.fctr")
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features,
cluster_vars)
}
# Last call for data modifications
#stop(here") # sav_allobs_df <- glb_allobs_df
# glb_allobs_df[(glb_allobs_df$PropR == 0.75) & (glb_allobs_df$State == "Hawaii"), "PropR.fctr"] <- "N"
# Re-partition
glb_trnobs_df <- subset(glb_allobs_df, .src == "Train")
glb_newobs_df <- subset(glb_allobs_df, .src == "Test")
glb_chunks_df <- myadd_chunk(glb_chunks_df, "select.features", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 7 manage.missing.data 4 1 38.829 38.973 0.144
## 8 select.features 5 0 38.973 NA NAStep 5.0: select features
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
print(glb_feats_df <- myselect_features(entity_df=glb_trnobs_df,
exclude_vars_as_features=glb_exclude_vars_as_features,
rsp_var=glb_rsp_var))## Warning in cor(data.matrix(entity_df[, sel_feats]), y =
## as.numeric(entity_df[, : the standard deviation is zero## id cor.y
## sold sold 1.0000000000
## biddable biddable 0.5485860292
## startprice startprice -0.4556701005
## UniqueID UniqueID -0.1904241613
## condition.fctr condition.fctr -0.1531007887
## D.npnct05.log D.npnct05.log -0.1178427734
## prdline.my.fctr prdline.my.fctr -0.0898840683
## D.npnct14.log D.npnct14.log -0.0784119354
## cellular.fctr cellular.fctr -0.0770423554
## carrier.fctr carrier.fctr -0.0677807650
## D.ndgts.log D.ndgts.log -0.0633901377
## D.nwrds.unq.log D.nwrds.unq.log -0.0619524203
## D.npnct09.log D.npnct09.log -0.0617301891
## D.nwrds.log D.nwrds.log -0.0587159086
## D.nchrs.log D.nchrs.log -0.0565815056
## D.ratio.nstopwrds.nwrds D.ratio.nstopwrds.nwrds 0.0554866401
## D.nuppr.log D.nuppr.log -0.0554742013
## D.npnct12.log D.npnct12.log -0.0549329137
## D.T.like D.T.like -0.0533938586
## D.npnct28.log D.npnct28.log -0.0523776347
## D.T.box D.T.box -0.0515596986
## D.npnct06.log D.npnct06.log -0.0497583609
## D.T.this D.T.this -0.0477867670
## D.npnct24.log D.npnct24.log -0.0459503420
## D.npnct16.log D.npnct16.log -0.0447153098
## D.nstopwrds.log D.nstopwrds.log -0.0439279746
## color.fctr color.fctr -0.0426291775
## D.T.condit D.T.condit -0.0415362400
## D.npnct15.log D.npnct15.log 0.0400921803
## D.npnct08.log D.npnct08.log -0.0394718187
## D.npnct13.log D.npnct13.log -0.0349433657
## D.T.screen D.T.screen 0.0312904991
## D.T.new D.T.new -0.0302966020
## D.sum.TfIdf D.sum.TfIdf -0.0300344031
## D.npnct03.log D.npnct03.log 0.0258721719
## D.T.used D.T.used 0.0251046087
## D.npnct10.log D.npnct10.log -0.0240301079
## D.T.ipad D.T.ipad -0.0234288421
## .rnorm .rnorm -0.0228561937
## D.npnct18.log D.npnct18.log -0.0214919447
## D.T.excellent D.T.excellent 0.0203632794
## D.npnct11.log D.npnct11.log -0.0188179512
## D.T.great D.T.great 0.0171206415
## D.ratio.sum.TfIdf.nwrds D.ratio.sum.TfIdf.nwrds 0.0119528209
## D.T.condition D.T.condition -0.0118174892
## D.P.mini D.P.mini -0.0111321924
## storage.fctr storage.fctr -0.0103459049
## D.T.use D.T.use -0.0097129508
## D.P.air D.P.air -0.0091681483
## D.T.scratch D.T.scratch -0.0091382072
## D.T.good D.T.good 0.0063426895
## D.npnct01.log D.npnct01.log 0.0042941114
## D.T.work D.T.work -0.0035586740
## D.T.veri D.T.veri -0.0001659508
## D.npnct02.log D.npnct02.log NA
## D.npnct04.log D.npnct04.log NA
## D.npnct07.log D.npnct07.log NA
## D.npnct17.log D.npnct17.log NA
## D.npnct19.log D.npnct19.log NA
## D.npnct20.log D.npnct20.log NA
## D.npnct21.log D.npnct21.log NA
## D.npnct22.log D.npnct22.log NA
## D.npnct23.log D.npnct23.log NA
## D.npnct25.log D.npnct25.log NA
## D.npnct26.log D.npnct26.log NA
## D.npnct27.log D.npnct27.log NA
## D.npnct29.log D.npnct29.log NA
## D.npnct30.log D.npnct30.log NA
## D.P.http D.P.http NA
## exclude.as.feat cor.y.abs
## sold 1 1.0000000000
## biddable 0 0.5485860292
## startprice 0 0.4556701005
## UniqueID 1 0.1904241613
## condition.fctr 0 0.1531007887
## D.npnct05.log 0 0.1178427734
## prdline.my.fctr 0 0.0898840683
## D.npnct14.log 0 0.0784119354
## cellular.fctr 0 0.0770423554
## carrier.fctr 0 0.0677807650
## D.ndgts.log 0 0.0633901377
## D.nwrds.unq.log 0 0.0619524203
## D.npnct09.log 0 0.0617301891
## D.nwrds.log 0 0.0587159086
## D.nchrs.log 0 0.0565815056
## D.ratio.nstopwrds.nwrds 0 0.0554866401
## D.nuppr.log 0 0.0554742013
## D.npnct12.log 0 0.0549329137
## D.T.like 0 0.0533938586
## D.npnct28.log 0 0.0523776347
## D.T.box 0 0.0515596986
## D.npnct06.log 0 0.0497583609
## D.T.this 0 0.0477867670
## D.npnct24.log 0 0.0459503420
## D.npnct16.log 0 0.0447153098
## D.nstopwrds.log 0 0.0439279746
## color.fctr 0 0.0426291775
## D.T.condit 0 0.0415362400
## D.npnct15.log 0 0.0400921803
## D.npnct08.log 0 0.0394718187
## D.npnct13.log 0 0.0349433657
## D.T.screen 0 0.0312904991
## D.T.new 0 0.0302966020
## D.sum.TfIdf 0 0.0300344031
## D.npnct03.log 0 0.0258721719
## D.T.used 0 0.0251046087
## D.npnct10.log 0 0.0240301079
## D.T.ipad 0 0.0234288421
## .rnorm 0 0.0228561937
## D.npnct18.log 0 0.0214919447
## D.T.excellent 0 0.0203632794
## D.npnct11.log 0 0.0188179512
## D.T.great 0 0.0171206415
## D.ratio.sum.TfIdf.nwrds 0 0.0119528209
## D.T.condition 0 0.0118174892
## D.P.mini 0 0.0111321924
## storage.fctr 0 0.0103459049
## D.T.use 0 0.0097129508
## D.P.air 0 0.0091681483
## D.T.scratch 0 0.0091382072
## D.T.good 0 0.0063426895
## D.npnct01.log 0 0.0042941114
## D.T.work 0 0.0035586740
## D.T.veri 0 0.0001659508
## D.npnct02.log 0 NA
## D.npnct04.log 0 NA
## D.npnct07.log 0 NA
## D.npnct17.log 0 NA
## D.npnct19.log 0 NA
## D.npnct20.log 0 NA
## D.npnct21.log 0 NA
## D.npnct22.log 0 NA
## D.npnct23.log 0 NA
## D.npnct25.log 0 NA
## D.npnct26.log 0 NA
## D.npnct27.log 0 NA
## D.npnct29.log 0 NA
## D.npnct30.log 0 NA
## D.P.http 0 NA# sav_feats_df <- glb_feats_df; glb_feats_df <- sav_feats_df
print(glb_feats_df <- orderBy(~-cor.y,
myfind_cor_features(feats_df=glb_feats_df, obs_df=glb_trnobs_df,
rsp_var=glb_rsp_var)))## [1] "cor(D.nchrs.log, D.nuppr.log)=0.9995"
## [1] "cor(sold.fctr, D.nchrs.log)=-0.0566"
## [1] "cor(sold.fctr, D.nuppr.log)=-0.0555"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.nuppr.log as highly correlated with
## D.nchrs.log## [1] "cor(D.nchrs.log, D.nwrds.log)=0.9931"
## [1] "cor(sold.fctr, D.nchrs.log)=-0.0566"
## [1] "cor(sold.fctr, D.nwrds.log)=-0.0587"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.nchrs.log as highly correlated with
## D.nwrds.log## [1] "cor(D.nwrds.log, D.nwrds.unq.log)=0.9892"
## [1] "cor(sold.fctr, D.nwrds.log)=-0.0587"
## [1] "cor(sold.fctr, D.nwrds.unq.log)=-0.0620"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.nwrds.log as highly correlated with
## D.nwrds.unq.log## [1] "cor(D.npnct24.log, D.ratio.nstopwrds.nwrds)=-0.9641"
## [1] "cor(sold.fctr, D.npnct24.log)=-0.0460"
## [1] "cor(sold.fctr, D.ratio.nstopwrds.nwrds)=0.0555"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.npnct24.log as highly correlated with
## D.ratio.nstopwrds.nwrds## [1] "cor(D.npnct06.log, D.npnct16.log)=0.9556"
## [1] "cor(sold.fctr, D.npnct06.log)=-0.0498"
## [1] "cor(sold.fctr, D.npnct16.log)=-0.0447"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.npnct16.log as highly correlated with
## D.npnct06.log## [1] "cor(D.nwrds.unq.log, D.sum.TfIdf)=0.9437"
## [1] "cor(sold.fctr, D.nwrds.unq.log)=-0.0620"
## [1] "cor(sold.fctr, D.sum.TfIdf)=-0.0300"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.sum.TfIdf as highly correlated with
## D.nwrds.unq.log## [1] "cor(D.nwrds.unq.log, D.ratio.nstopwrds.nwrds)=-0.9223"
## [1] "cor(sold.fctr, D.nwrds.unq.log)=-0.0620"
## [1] "cor(sold.fctr, D.ratio.nstopwrds.nwrds)=0.0555"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.ratio.nstopwrds.nwrds as highly correlated
## with D.nwrds.unq.log## [1] "cor(D.nstopwrds.log, D.nwrds.unq.log)=0.8970"
## [1] "cor(sold.fctr, D.nstopwrds.log)=-0.0439"
## [1] "cor(sold.fctr, D.nwrds.unq.log)=-0.0620"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.nstopwrds.log as highly correlated with
## D.nwrds.unq.log## [1] "cor(carrier.fctr, cellular.fctr)=0.8345"
## [1] "cor(sold.fctr, carrier.fctr)=-0.0678"
## [1] "cor(sold.fctr, cellular.fctr)=-0.0770"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified carrier.fctr as highly correlated with
## cellular.fctr## [1] "cor(D.npnct13.log, D.nwrds.unq.log)=0.7214"
## [1] "cor(sold.fctr, D.npnct13.log)=-0.0349"
## [1] "cor(sold.fctr, D.nwrds.unq.log)=-0.0620"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.npnct13.log as highly correlated with
## D.nwrds.unq.log## [1] "cor(D.T.like, D.T.new)=0.7047"
## [1] "cor(sold.fctr, D.T.like)=-0.0534"
## [1] "cor(sold.fctr, D.T.new)=-0.0303"## Warning in myfind_cor_features(feats_df = glb_feats_df, obs_df =
## glb_trnobs_df, : Identified D.T.new as highly correlated with D.T.like## id cor.y exclude.as.feat cor.y.abs
## 66 sold 1.0000000000 1 1.0000000000
## 2 biddable 0.5485860292 0 0.5485860292
## 46 D.ratio.nstopwrds.nwrds 0.0554866401 0 0.0554866401
## 23 D.npnct15.log 0.0400921803 0 0.0400921803
## 59 D.T.screen 0.0312904991 0 0.0312904991
## 11 D.npnct03.log 0.0258721719 0 0.0258721719
## 62 D.T.used 0.0251046087 0 0.0251046087
## 52 D.T.excellent 0.0203632794 0 0.0203632794
## 54 D.T.great 0.0171206415 0 0.0171206415
## 47 D.ratio.sum.TfIdf.nwrds 0.0119528209 0 0.0119528209
## 53 D.T.good 0.0063426895 0 0.0063426895
## 9 D.npnct01.log 0.0042941114 0 0.0042941114
## 63 D.T.veri -0.0001659508 0 0.0001659508
## 64 D.T.work -0.0035586740 0 0.0035586740
## 58 D.T.scratch -0.0091382072 0 0.0091382072
## 43 D.P.air -0.0091681483 0 0.0091681483
## 61 D.T.use -0.0097129508 0 0.0097129508
## 68 storage.fctr -0.0103459049 0 0.0103459049
## 45 D.P.mini -0.0111321924 0 0.0111321924
## 51 D.T.condition -0.0118174892 0 0.0118174892
## 19 D.npnct11.log -0.0188179512 0 0.0188179512
## 26 D.npnct18.log -0.0214919447 0 0.0214919447
## 1 .rnorm -0.0228561937 0 0.0228561937
## 55 D.T.ipad -0.0234288421 0 0.0234288421
## 18 D.npnct10.log -0.0240301079 0 0.0240301079
## 48 D.sum.TfIdf -0.0300344031 0 0.0300344031
## 57 D.T.new -0.0302966020 0 0.0302966020
## 21 D.npnct13.log -0.0349433657 0 0.0349433657
## 16 D.npnct08.log -0.0394718187 0 0.0394718187
## 50 D.T.condit -0.0415362400 0 0.0415362400
## 5 color.fctr -0.0426291775 0 0.0426291775
## 39 D.nstopwrds.log -0.0439279746 0 0.0439279746
## 24 D.npnct16.log -0.0447153098 0 0.0447153098
## 32 D.npnct24.log -0.0459503420 0 0.0459503420
## 60 D.T.this -0.0477867670 0 0.0477867670
## 14 D.npnct06.log -0.0497583609 0 0.0497583609
## 49 D.T.box -0.0515596986 0 0.0515596986
## 36 D.npnct28.log -0.0523776347 0 0.0523776347
## 56 D.T.like -0.0533938586 0 0.0533938586
## 20 D.npnct12.log -0.0549329137 0 0.0549329137
## 40 D.nuppr.log -0.0554742013 0 0.0554742013
## 7 D.nchrs.log -0.0565815056 0 0.0565815056
## 41 D.nwrds.log -0.0587159086 0 0.0587159086
## 17 D.npnct09.log -0.0617301891 0 0.0617301891
## 42 D.nwrds.unq.log -0.0619524203 0 0.0619524203
## 8 D.ndgts.log -0.0633901377 0 0.0633901377
## 3 carrier.fctr -0.0677807650 0 0.0677807650
## 4 cellular.fctr -0.0770423554 0 0.0770423554
## 22 D.npnct14.log -0.0784119354 0 0.0784119354
## 65 prdline.my.fctr -0.0898840683 0 0.0898840683
## 13 D.npnct05.log -0.1178427734 0 0.1178427734
## 6 condition.fctr -0.1531007887 0 0.1531007887
## 69 UniqueID -0.1904241613 1 0.1904241613
## 67 startprice -0.4556701005 0 0.4556701005
## 10 D.npnct02.log NA 0 NA
## 12 D.npnct04.log NA 0 NA
## 15 D.npnct07.log NA 0 NA
## 25 D.npnct17.log NA 0 NA
## 27 D.npnct19.log NA 0 NA
## 28 D.npnct20.log NA 0 NA
## 29 D.npnct21.log NA 0 NA
## 30 D.npnct22.log NA 0 NA
## 31 D.npnct23.log NA 0 NA
## 33 D.npnct25.log NA 0 NA
## 34 D.npnct26.log NA 0 NA
## 35 D.npnct27.log NA 0 NA
## 37 D.npnct29.log NA 0 NA
## 38 D.npnct30.log NA 0 NA
## 44 D.P.http NA 0 NA
## cor.high.X freqRatio percentUnique zeroVar nzv
## 66 <NA> 1.163953 0.10746910 FALSE FALSE
## 2 <NA> 1.223417 0.10746910 FALSE FALSE
## 46 D.nwrds.unq.log 13.387500 4.67490596 FALSE FALSE
## 23 <NA> 153.500000 0.16120365 FALSE TRUE
## 59 <NA> 45.105263 0.80601827 FALSE TRUE
## 11 <NA> 83.318182 0.16120365 FALSE TRUE
## 62 <NA> 161.818182 0.85975282 FALSE TRUE
## 52 <NA> 227.875000 0.80601827 FALSE TRUE
## 54 <NA> 127.214286 0.75228372 FALSE TRUE
## 47 <NA> 63.294118 35.14239656 FALSE FALSE
## 53 <NA> 39.181818 1.02095648 FALSE TRUE
## 9 <NA> 53.029412 0.32240731 FALSE TRUE
## 63 <NA> 163.090909 0.85975282 FALSE TRUE
## 64 <NA> 82.761905 0.91348737 FALSE TRUE
## 58 <NA> 35.416667 0.80601827 FALSE TRUE
## 43 <NA> 123.000000 0.16120365 FALSE TRUE
## 61 <NA> 57.533333 0.96722192 FALSE TRUE
## 68 <NA> 2.739003 0.26867276 FALSE FALSE
## 45 <NA> 92.000000 0.16120365 FALSE TRUE
## 51 <NA> 52.375000 0.80601827 FALSE TRUE
## 19 <NA> 9.385965 0.37614186 FALSE FALSE
## 26 <NA> 1860.000000 0.10746910 FALSE TRUE
## 1 <NA> 1.000000 100.00000000 FALSE FALSE
## 55 <NA> 51.484848 0.91348737 FALSE TRUE
## 18 <NA> 309.000000 0.16120365 FALSE TRUE
## 48 D.nwrds.unq.log 63.294118 34.87372380 FALSE FALSE
## 57 D.T.like 147.166667 0.91348737 FALSE TRUE
## 21 D.nwrds.unq.log 5.210728 0.48361096 FALSE FALSE
## 16 <NA> 69.653846 0.21493821 FALSE TRUE
## 50 <NA> 52.000000 0.85975282 FALSE TRUE
## 5 <NA> 1.576837 0.26867276 FALSE FALSE
## 39 D.nwrds.unq.log 14.144578 0.80601827 FALSE FALSE
## 24 D.npnct06.log 31.280702 0.16120365 FALSE TRUE
## 32 D.ratio.nstopwrds.nwrds 1.355696 0.10746910 FALSE FALSE
## 60 <NA> 40.744186 0.69854917 FALSE TRUE
## 14 <NA> 33.773585 0.16120365 FALSE TRUE
## 49 <NA> 111.875000 0.85975282 FALSE TRUE
## 36 <NA> 463.750000 0.16120365 FALSE TRUE
## 56 <NA> 259.142857 0.85975282 FALSE TRUE
## 20 <NA> 27.261538 0.21493821 FALSE TRUE
## 40 D.nchrs.log 16.507692 4.35249866 FALSE FALSE
## 7 D.nwrds.log 14.875000 5.64212789 FALSE FALSE
## 41 D.nwrds.unq.log 12.310345 1.39709833 FALSE FALSE
## 17 <NA> 308.666667 0.21493821 FALSE TRUE
## 42 <NA> 7.685714 0.91348737 FALSE FALSE
## 8 <NA> 27.063492 0.69854917 FALSE TRUE
## 3 cellular.fctr 3.192529 0.37614186 FALSE FALSE
## 4 <NA> 2.128846 0.16120365 FALSE FALSE
## 22 <NA> 35.372549 0.26867276 FALSE TRUE
## 65 <NA> 1.032258 0.64481462 FALSE FALSE
## 13 <NA> 40.355556 0.10746910 FALSE TRUE
## 6 <NA> 4.006920 0.32240731 FALSE FALSE
## 69 <NA> 1.000000 100.00000000 FALSE FALSE
## 67 <NA> 2.807692 30.14508329 FALSE FALSE
## 10 <NA> 0.000000 0.05373455 TRUE TRUE
## 12 <NA> 0.000000 0.05373455 TRUE TRUE
## 15 <NA> 0.000000 0.05373455 TRUE TRUE
## 25 <NA> 0.000000 0.05373455 TRUE TRUE
## 27 <NA> 0.000000 0.05373455 TRUE TRUE
## 28 <NA> 0.000000 0.05373455 TRUE TRUE
## 29 <NA> 0.000000 0.05373455 TRUE TRUE
## 30 <NA> 0.000000 0.05373455 TRUE TRUE
## 31 <NA> 0.000000 0.05373455 TRUE TRUE
## 33 <NA> 0.000000 0.05373455 TRUE TRUE
## 34 <NA> 0.000000 0.05373455 TRUE TRUE
## 35 <NA> 0.000000 0.05373455 TRUE TRUE
## 37 <NA> 0.000000 0.05373455 TRUE TRUE
## 38 <NA> 0.000000 0.05373455 TRUE TRUE
## 44 <NA> 0.000000 0.05373455 TRUE TRUE
## myNearZV is.cor.y.abs.low
## 66 FALSE FALSE
## 2 FALSE FALSE
## 46 FALSE FALSE
## 23 FALSE FALSE
## 59 FALSE FALSE
## 11 FALSE FALSE
## 62 FALSE FALSE
## 52 FALSE TRUE
## 54 FALSE TRUE
## 47 FALSE TRUE
## 53 FALSE TRUE
## 9 FALSE TRUE
## 63 FALSE TRUE
## 64 FALSE TRUE
## 58 FALSE TRUE
## 43 FALSE TRUE
## 61 FALSE TRUE
## 68 FALSE TRUE
## 45 FALSE TRUE
## 51 FALSE TRUE
## 19 FALSE TRUE
## 26 TRUE TRUE
## 1 FALSE FALSE
## 55 FALSE FALSE
## 18 FALSE FALSE
## 48 FALSE FALSE
## 57 FALSE FALSE
## 21 FALSE FALSE
## 16 FALSE FALSE
## 50 FALSE FALSE
## 5 FALSE FALSE
## 39 FALSE FALSE
## 24 FALSE FALSE
## 32 FALSE FALSE
## 60 FALSE FALSE
## 14 FALSE FALSE
## 49 FALSE FALSE
## 36 FALSE FALSE
## 56 FALSE FALSE
## 20 FALSE FALSE
## 40 FALSE FALSE
## 7 FALSE FALSE
## 41 FALSE FALSE
## 17 FALSE FALSE
## 42 FALSE FALSE
## 8 FALSE FALSE
## 3 FALSE FALSE
## 4 FALSE FALSE
## 22 FALSE FALSE
## 65 FALSE FALSE
## 13 FALSE FALSE
## 6 FALSE FALSE
## 69 FALSE FALSE
## 67 FALSE FALSE
## 10 TRUE NA
## 12 TRUE NA
## 15 TRUE NA
## 25 TRUE NA
## 27 TRUE NA
## 28 TRUE NA
## 29 TRUE NA
## 30 TRUE NA
## 31 TRUE NA
## 33 TRUE NA
## 34 TRUE NA
## 35 TRUE NA
## 37 TRUE NA
## 38 TRUE NA
## 44 TRUE NA#subset(glb_feats_df, id %in% c("A.nuppr.log", "S.nuppr.log"))
print(myplot_scatter(glb_feats_df, "percentUnique", "freqRatio",
colorcol_name="myNearZV", jitter=TRUE) +
geom_point(aes(shape=nzv)) + xlim(-5, 25))## Warning in myplot_scatter(glb_feats_df, "percentUnique", "freqRatio",
## colorcol_name = "myNearZV", : converting myNearZV to class:factor## Warning: Removed 5 rows containing missing values (geom_point).## Warning: Removed 5 rows containing missing values (geom_point).## Warning: Removed 5 rows containing missing values (geom_point).
print(subset(glb_feats_df, myNearZV))## id cor.y exclude.as.feat cor.y.abs cor.high.X
## 26 D.npnct18.log -0.02149194 0 0.02149194 <NA>
## 10 D.npnct02.log NA 0 NA <NA>
## 12 D.npnct04.log NA 0 NA <NA>
## 15 D.npnct07.log NA 0 NA <NA>
## 25 D.npnct17.log NA 0 NA <NA>
## 27 D.npnct19.log NA 0 NA <NA>
## 28 D.npnct20.log NA 0 NA <NA>
## 29 D.npnct21.log NA 0 NA <NA>
## 30 D.npnct22.log NA 0 NA <NA>
## 31 D.npnct23.log NA 0 NA <NA>
## 33 D.npnct25.log NA 0 NA <NA>
## 34 D.npnct26.log NA 0 NA <NA>
## 35 D.npnct27.log NA 0 NA <NA>
## 37 D.npnct29.log NA 0 NA <NA>
## 38 D.npnct30.log NA 0 NA <NA>
## 44 D.P.http NA 0 NA <NA>
## freqRatio percentUnique zeroVar nzv myNearZV is.cor.y.abs.low
## 26 1860 0.10746910 FALSE TRUE TRUE TRUE
## 10 0 0.05373455 TRUE TRUE TRUE NA
## 12 0 0.05373455 TRUE TRUE TRUE NA
## 15 0 0.05373455 TRUE TRUE TRUE NA
## 25 0 0.05373455 TRUE TRUE TRUE NA
## 27 0 0.05373455 TRUE TRUE TRUE NA
## 28 0 0.05373455 TRUE TRUE TRUE NA
## 29 0 0.05373455 TRUE TRUE TRUE NA
## 30 0 0.05373455 TRUE TRUE TRUE NA
## 31 0 0.05373455 TRUE TRUE TRUE NA
## 33 0 0.05373455 TRUE TRUE TRUE NA
## 34 0 0.05373455 TRUE TRUE TRUE NA
## 35 0 0.05373455 TRUE TRUE TRUE NA
## 37 0 0.05373455 TRUE TRUE TRUE NA
## 38 0 0.05373455 TRUE TRUE TRUE NA
## 44 0 0.05373455 TRUE TRUE TRUE NAglb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df),
subset(glb_feats_df, myNearZV)$id)]
glb_trnobs_df <- subset(glb_allobs_df, .src == "Train")
glb_newobs_df <- subset(glb_allobs_df, .src == "Test")
if (!is.null(glb_interaction_only_features))
glb_feats_df[glb_feats_df$id %in% glb_interaction_only_features, "interaction.feat"] <-
names(glb_interaction_only_features) else
glb_feats_df$interaction.feat <- NA
mycheck_problem_data(glb_allobs_df, terminate = TRUE)## [1] "numeric data missing in : "
## sold sold.fctr
## 798 798
## [1] "numeric data w/ 0s in : "
## biddable sold cellular.fctr
## 1446 1001 1595
## D.T.condit D.T.condition D.T.good
## 2455 2385 2463
## D.T.ipad D.T.new D.T.scratch
## 2432 2520 2431
## D.T.screen D.T.this D.T.use
## 2453 2503 2474
## D.T.work D.T.box D.T.excellent
## 2485 2553 2602
## D.T.great D.T.like D.T.used
## 2539 2591 2540
## D.T.veri D.nwrds.log D.nwrds.unq.log
## 2567 1521 1529
## D.sum.TfIdf D.ratio.sum.TfIdf.nwrds D.nchrs.log
## 1529 1529 1521
## D.nuppr.log D.ndgts.log D.npnct01.log
## 1523 2428 2581
## D.npnct03.log D.npnct05.log D.npnct06.log
## 2616 2594 2556
## D.npnct08.log D.npnct09.log D.npnct10.log
## 2583 2643 2650
## D.npnct11.log D.npnct12.log D.npnct13.log
## 2303 2539 1934
## D.npnct14.log D.npnct15.log D.npnct16.log
## 2584 2638 2548
## D.npnct24.log D.npnct28.log D.nstopwrds.log
## 1521 2651 1669
## D.P.mini D.P.air
## 2625 2639
## [1] "numeric data w/ Infs in : "
## named integer(0)
## [1] "numeric data w/ NaNs in : "
## named integer(0)
## [1] "string data missing in : "
## description condition cellular carrier color storage
## 1521 0 0 0 0 0
## productline prdline.my
## 0 0# glb_allobs_df %>% filter(is.na(Married.fctr)) %>% tbl_df()
# glb_allobs_df %>% count(Married.fctr)
# levels(glb_allobs_df$Married.fctr)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "partition.data.training", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 8 select.features 5 0 38.973 40.432 1.46
## 9 partition.data.training 6 0 40.433 NA NAStep 6.0: partition data training
if (all(is.na(glb_newobs_df[, glb_rsp_var]))) {
set.seed(glb_split_sample.seed)
OOB_size <- nrow(glb_newobs_df) * 1.1
if (is.null(glb_category_vars)) {
require(caTools)
split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw],
SplitRatio=OOB_size / nrow(glb_trnobs_df))
glb_OOBobs_df <- glb_trnobs_df[split ,]
glb_fitobs_df <- glb_trnobs_df[!split, ]
} else {
sample_vars <- c(glb_rsp_var_raw, glb_category_vars)
rspvar_freq_df <- orderBy(reformulate(glb_rsp_var_raw),
mycreate_sqlxtab_df(glb_trnobs_df, glb_rsp_var_raw))
OOB_rspvar_size <- 1.0 * OOB_size * rspvar_freq_df$.n / sum(rspvar_freq_df$.n)
newobs_freq_df <- orderBy(reformulate(glb_category_vars),
mycreate_sqlxtab_df(glb_newobs_df, glb_category_vars))
trnobs_freq_df <- orderBy(reformulate(glb_category_vars),
mycreate_sqlxtab_df(glb_trnobs_df, glb_category_vars))
allobs_freq_df <- merge(newobs_freq_df, trnobs_freq_df, by=glb_category_vars,
all=TRUE, sort=TRUE, suffixes=c(".Tst", ".Train"))
allobs_freq_df[is.na(allobs_freq_df)] <- 0
OOB_strata_size <- ceiling(
as.vector(matrix(allobs_freq_df$.n.Tst * 1.0 / sum(allobs_freq_df$.n.Tst)) %*%
matrix(OOB_rspvar_size, nrow=1)))
OOB_strata_size[OOB_strata_size == 0] <- 1
OOB_strata_df <- expand.grid(glb_rsp_var_raw=rspvar_freq_df[, glb_rsp_var_raw],
glb_category_vars=allobs_freq_df[, glb_category_vars])
names(OOB_strata_df) <- sample_vars
OOB_strata_df <- orderBy(reformulate(sample_vars), OOB_strata_df)
trnobs_univ_df <- orderBy(reformulate(sample_vars),
mycreate_sqlxtab_df(glb_trnobs_df, sample_vars))
trnobs_univ_df <- merge(trnobs_univ_df, OOB_strata_df, all=TRUE)
tmp_trnobs_df <- orderBy(reformulate(c(glb_rsp_var_raw, glb_category_vars)),
glb_trnobs_df)
require(sampling)
split_strata <- strata(tmp_trnobs_df,
stratanames=c(glb_rsp_var_raw, glb_category_vars),
size=OOB_strata_size[!is.na(trnobs_univ_df$.n)],
method="srswor")
glb_OOBobs_df <- getdata(tmp_trnobs_df, split_strata)[, names(glb_trnobs_df)]
glb_fitobs_df <- glb_trnobs_df[!glb_trnobs_df[, glb_id_var] %in%
glb_OOBobs_df[, glb_id_var], ]
}
} else {
print(sprintf("Newdata contains non-NA data for %s; setting OOB to Newdata",
glb_rsp_var))
glb_fitobs_df <- glb_trnobs_df; glb_OOBobs_df <- glb_newobs_df
}## Loading required package: sampling
##
## Attaching package: 'sampling'
##
## The following objects are masked from 'package:survival':
##
## cluster, strata
##
## The following object is masked from 'package:caret':
##
## clusterif (!is.null(glb_max_fitobs) && (nrow(glb_fitobs_df) > glb_max_fitobs)) {
warning("glb_fitobs_df restricted to glb_max_fitobs: ",
format(glb_max_fitobs, big.mark=","))
org_fitobs_df <- glb_fitobs_df
glb_fitobs_df <-
org_fitobs_df[split <- sample.split(org_fitobs_df[, glb_rsp_var_raw],
SplitRatio=glb_max_fitobs), ]
org_fitobs_df <- NULL
}
glb_allobs_df$.lcn <- ""
glb_allobs_df[glb_allobs_df[, glb_id_var] %in%
glb_fitobs_df[, glb_id_var], ".lcn"] <- "Fit"
glb_allobs_df[glb_allobs_df[, glb_id_var] %in%
glb_OOBobs_df[, glb_id_var], ".lcn"] <- "OOB"
dsp_class_dstrb <- function(obs_df, location_var, partition_var) {
xtab_df <- mycreate_xtab_df(obs_df, c(location_var, partition_var))
rownames(xtab_df) <- xtab_df[, location_var]
xtab_df <- xtab_df[, -grepl(location_var, names(xtab_df))]
print(xtab_df)
print(xtab_df / rowSums(xtab_df, na.rm=TRUE))
}
# Ensure proper splits by glb_rsp_var_raw & user-specified feature for OOB vs. new
if (!is.null(glb_category_vars)) {
if (glb_is_classification)
dsp_class_dstrb(glb_allobs_df, ".lcn", glb_rsp_var_raw)
newobs_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .src == "Test"),
glb_category_vars)
OOBobs_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .lcn == "OOB"),
glb_category_vars)
glb_ctgry_df <- merge(newobs_ctgry_df, OOBobs_ctgry_df, by=glb_category_vars
, all=TRUE, suffixes=c(".Tst", ".OOB"))
glb_ctgry_df$.freqRatio.Tst <- glb_ctgry_df$.n.Tst / sum(glb_ctgry_df$.n.Tst, na.rm=TRUE)
glb_ctgry_df$.freqRatio.OOB <- glb_ctgry_df$.n.OOB / sum(glb_ctgry_df$.n.OOB, na.rm=TRUE)
print(orderBy(~-.freqRatio.Tst-.freqRatio.OOB, glb_ctgry_df))
}## sold.0 sold.1 sold.NA
## NA NA 798
## Fit 522 447 NA
## OOB 479 413 NA
## sold.0 sold.1 sold.NA
## NA NA 1
## Fit 0.5386997 0.4613003 NA
## OOB 0.5369955 0.4630045 NA
## prdline.my .n.Tst .n.OOB .freqRatio.Tst .freqRatio.OOB
## 2 iPad 2 154 171 0.19298246 0.191704036
## 8 iPad mini 114 126 0.14285714 0.141255605
## 1 iPad 1 89 99 0.11152882 0.110986547
## 12 Unknown 87 97 0.10902256 0.108744395
## 6 iPad Air 75 84 0.09398496 0.094170404
## 4 iPad 4 68 76 0.08521303 0.085201794
## 7 iPad Air 2 62 69 0.07769424 0.077354260
## 9 iPad mini 2 56 63 0.07017544 0.070627803
## 3 iPad 3 55 61 0.06892231 0.068385650
## 10 iPad mini 3 38 43 0.04761905 0.048206278
## 11 iPad mini Retina NA 2 NA 0.002242152
## 5 iPad 5 NA 1 NA 0.001121076# Run this line by line
print("glb_feats_df:"); print(dim(glb_feats_df))## [1] "glb_feats_df:"## [1] 69 12sav_feats_df <- glb_feats_df
glb_feats_df <- sav_feats_df
glb_feats_df[, "rsp_var_raw"] <- FALSE
glb_feats_df[glb_feats_df$id == glb_rsp_var_raw, "rsp_var_raw"] <- TRUE
glb_feats_df$exclude.as.feat <- (glb_feats_df$exclude.as.feat == 1)
if (!is.null(glb_id_var) && glb_id_var != ".rownames")
glb_feats_df[glb_feats_df$id %in% glb_id_var, "id_var"] <- TRUE
add_feats_df <- data.frame(id=glb_rsp_var, exclude.as.feat=TRUE, rsp_var=TRUE)
row.names(add_feats_df) <- add_feats_df$id; print(add_feats_df)## id exclude.as.feat rsp_var
## sold.fctr sold.fctr TRUE TRUEglb_feats_df <- myrbind_df(glb_feats_df, add_feats_df)
if (glb_id_var != ".rownames")
print(subset(glb_feats_df, rsp_var_raw | rsp_var | id_var)) else
print(subset(glb_feats_df, rsp_var_raw | rsp_var)) ## id cor.y exclude.as.feat cor.y.abs cor.high.X
## 66 sold 1.0000000 TRUE 1.0000000 <NA>
## 69 UniqueID -0.1904242 TRUE 0.1904242 <NA>
## sold.fctr sold.fctr NA TRUE NA <NA>
## freqRatio percentUnique zeroVar nzv myNearZV is.cor.y.abs.low
## 66 1.163953 0.1074691 FALSE FALSE FALSE FALSE
## 69 1.000000 100.0000000 FALSE FALSE FALSE FALSE
## sold.fctr NA NA NA NA NA NA
## interaction.feat rsp_var_raw id_var rsp_var
## 66 NA TRUE NA NA
## 69 NA FALSE TRUE NA
## sold.fctr NA NA NA TRUEprint("glb_feats_df vs. glb_allobs_df: "); ## [1] "glb_feats_df vs. glb_allobs_df: "print(setdiff(glb_feats_df$id, names(glb_allobs_df)))## [1] "D.npnct18.log" "D.npnct02.log" "D.npnct04.log" "D.npnct07.log"
## [5] "D.npnct17.log" "D.npnct19.log" "D.npnct20.log" "D.npnct21.log"
## [9] "D.npnct22.log" "D.npnct23.log" "D.npnct25.log" "D.npnct26.log"
## [13] "D.npnct27.log" "D.npnct29.log" "D.npnct30.log" "D.P.http"print("glb_allobs_df vs. glb_feats_df: "); ## [1] "glb_allobs_df vs. glb_feats_df: "# Ensure these are only chr vars
print(setdiff(setdiff(names(glb_allobs_df), glb_feats_df$id),
myfind_chr_cols_df(glb_allobs_df)))## character(0)#print(setdiff(setdiff(names(glb_allobs_df), glb_exclude_vars_as_features),
# glb_feats_df$id))
print("glb_allobs_df: "); print(dim(glb_allobs_df))## [1] "glb_allobs_df: "## [1] 2659 64print("glb_trnobs_df: "); print(dim(glb_trnobs_df))## [1] "glb_trnobs_df: "## [1] 1861 63print("glb_fitobs_df: "); print(dim(glb_fitobs_df))## [1] "glb_fitobs_df: "## [1] 969 63print("glb_OOBobs_df: "); print(dim(glb_OOBobs_df))## [1] "glb_OOBobs_df: "## [1] 892 63print("glb_newobs_df: "); print(dim(glb_newobs_df))## [1] "glb_newobs_df: "## [1] 798 63# # Does not handle NULL or length(glb_id_var) > 1
# glb_allobs_df$.src.trn <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_trnobs_df[, glb_id_var],
# ".src.trn"] <- 1
# glb_allobs_df$.src.fit <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_fitobs_df[, glb_id_var],
# ".src.fit"] <- 1
# glb_allobs_df$.src.OOB <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_OOBobs_df[, glb_id_var],
# ".src.OOB"] <- 1
# glb_allobs_df$.src.new <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_newobs_df[, glb_id_var],
# ".src.new"] <- 1
# #print(unique(glb_allobs_df[, ".src.trn"]))
# write_cols <- c(glb_feats_df$id,
# ".src.trn", ".src.fit", ".src.OOB", ".src.new")
# glb_allobs_df <- glb_allobs_df[, write_cols]
#
# tmp_feats_df <- glb_feats_df
# tmp_entity_df <- glb_allobs_df
if (glb_save_envir)
save(glb_feats_df,
glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
file=paste0(glb_out_pfx, "blddfs_dsk.RData"))
# load(paste0(glb_out_pfx, "blddfs_dsk.RData"))
# if (!all.equal(tmp_feats_df, glb_feats_df))
# stop("glb_feats_df r/w not working")
# if (!all.equal(tmp_entity_df, glb_allobs_df))
# stop("glb_allobs_df r/w not working")
rm(split)## Warning in rm(split): object 'split' not foundglb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 9 partition.data.training 6 0 40.433 41.384 0.951
## 10 fit.models 7 0 41.384 NA NAStep 7.0: fit models
# load(paste0(glb_out_pfx, "dsk.RData"))
# keep_cols <- setdiff(names(glb_allobs_df),
# grep("^.src", names(glb_allobs_df), value=TRUE))
# glb_trnobs_df <- glb_allobs_df[glb_allobs_df$.src.trn == 1, keep_cols]
# glb_fitobs_df <- glb_allobs_df[glb_allobs_df$.src.fit == 1, keep_cols]
# glb_OOBobs_df <- glb_allobs_df[glb_allobs_df$.src.OOB == 1, keep_cols]
# glb_newobs_df <- glb_allobs_df[glb_allobs_df$.src.new == 1, keep_cols]
#
# glb_models_lst <- list(); glb_models_df <- data.frame()
#
if (glb_is_classification && glb_is_binomial &&
(length(unique(glb_fitobs_df[, glb_rsp_var])) < 2))
stop("glb_fitobs_df$", glb_rsp_var, ": contains less than 2 unique values: ",
paste0(unique(glb_fitobs_df[, glb_rsp_var]), collapse=", "))
max_cor_y_x_vars <- orderBy(~ -cor.y.abs,
subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low &
is.na(cor.high.X)))[1:2, "id"]
# while(length(max_cor_y_x_vars) < 2) {
# max_cor_y_x_vars <- c(max_cor_y_x_vars, orderBy(~ -cor.y.abs,
# subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low))[3, "id"])
# }
if (!is.null(glb_Baseline_mdl_var)) {
if ((max_cor_y_x_vars[1] != glb_Baseline_mdl_var) &
(glb_feats_df[glb_feats_df$id == max_cor_y_x_vars[1], "cor.y.abs"] >
glb_feats_df[glb_feats_df$id == glb_Baseline_mdl_var, "cor.y.abs"]))
stop(max_cor_y_x_vars[1], " has a higher correlation with ", glb_rsp_var,
" than the Baseline var: ", glb_Baseline_mdl_var)
}
glb_model_type <- ifelse(glb_is_regression, "regression", "classification")
# Baseline
if (!is.null(glb_Baseline_mdl_var))
ret_lst <- myfit_mdl(model_id="Baseline",
model_method="mybaseln_classfr",
indep_vars_vctr=glb_Baseline_mdl_var,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
# Most Frequent Outcome "MFO" model: mean(y) for regression
# Not using caret's nullModel since model stats not avl
# Cannot use rpart for multinomial classification since it predicts non-MFO
ret_lst <- myfit_mdl(model_id="MFO",
model_method=ifelse(glb_is_regression, "lm", "myMFO_classfr"),
model_type=glb_model_type,
indep_vars_vctr=".rnorm",
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)## [1] "fitting model: MFO.myMFO_classfr"
## [1] " indep_vars: .rnorm"
## Fitting parameter = none on full training set
## [1] "in MFO.Classifier$fit"
## [1] "unique.vals:"
## [1] N Y
## Levels: N Y
## [1] "unique.prob:"
## y
## N Y
## 0.5386997 0.4613003
## [1] "MFO.val:"
## [1] "N"
## Length Class Mode
## unique.vals 2 factor numeric
## unique.prob 2 -none- numeric
## MFO.val 1 -none- character
## x.names 1 -none- character
## xNames 1 -none- character
## problemType 1 -none- character
## tuneValue 1 data.frame list
## obsLevels 2 -none- character
## [1] " calling mypredict_mdl for fit:"## Loading required package: ROCR
## Loading required package: gplots
##
## Attaching package: 'gplots'
##
## The following object is masked from 'package:stats':
##
## lowess## [1] "in MFO.Classifier$prob"
## N Y
## 1 0.5386997 0.4613003
## 2 0.5386997 0.4613003
## 3 0.5386997 0.4613003
## 4 0.5386997 0.4613003
## 5 0.5386997 0.4613003
## 6 0.5386997 0.4613003
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.MFO.myMFO_classfr.N
## 1 N 522
## 2 Y 447
## Prediction
## Reference N Y
## N 522 0
## Y 447 0
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5.386997e-01 0.000000e+00 5.067192e-01 5.704443e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 5.131824e-01 8.826336e-99
## [1] " calling mypredict_mdl for OOB:"
## [1] "in MFO.Classifier$prob"
## N Y
## 1 0.5386997 0.4613003
## 2 0.5386997 0.4613003
## 3 0.5386997 0.4613003
## 4 0.5386997 0.4613003
## 5 0.5386997 0.4613003
## 6 0.5386997 0.4613003
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.MFO.myMFO_classfr.N
## 1 N 479
## 2 Y 413
## Prediction
## Reference N Y
## N 479 0
## Y 413 0
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5.369955e-01 0.000000e+00 5.036362e-01 5.701097e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 5.137205e-01 2.217817e-91
## model_id model_method feats max.nTuningRuns
## 1 MFO.myMFO_classfr myMFO_classfr .rnorm 0
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.387 0.003 0.5
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.5 0 0.5386997
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.5067192 0.5704443 0 0.5
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.5 0 0.5369955
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.5036362 0.5701097 0if (glb_is_classification)
# "random" model - only for classification;
# none needed for regression since it is same as MFO
ret_lst <- myfit_mdl(model_id="Random", model_method="myrandom_classfr",
model_type=glb_model_type,
indep_vars_vctr=".rnorm",
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)## [1] "fitting model: Random.myrandom_classfr"
## [1] " indep_vars: .rnorm"
## Fitting parameter = none on full training set
## Length Class Mode
## unique.vals 2 factor numeric
## unique.prob 2 table numeric
## xNames 1 -none- character
## problemType 1 -none- character
## tuneValue 1 data.frame list
## obsLevels 2 -none- character
## [1] " calling mypredict_mdl for fit:"
## [1] "in Random.Classifier$prob"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.6313559
## 3 0.2 0.6313559
## 4 0.3 0.6313559
## 5 0.4 0.6313559
## 6 0.5 0.4523282
## 7 0.6 0.0000000
## 8 0.7 0.0000000
## 9 0.8 0.0000000
## 10 0.9 0.0000000
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Random.myrandom_classfr.Y
## 1 N 522
## 2 Y 447
## Prediction
## Reference N Y
## N 0 522
## Y 0 447
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 4.613003e-01 0.000000e+00 4.295557e-01 4.932808e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 9.999994e-01 4.227904e-115
## [1] " calling mypredict_mdl for OOB:"
## [1] "in Random.Classifier$prob"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6329502
## 3 0.2 0.6329502
## 4 0.3 0.6329502
## 5 0.4 0.6329502
## 6 0.5 0.4830097
## 7 0.6 0.0000000
## 8 0.7 0.0000000
## 9 0.8 0.0000000
## 10 0.9 0.0000000
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Random.myrandom_classfr.Y
## 1 N 479
## 2 Y 413
## Prediction
## Reference N Y
## N 0 479
## Y 0 413
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 4.630045e-01 0.000000e+00 4.298903e-01 4.963638e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 9.999959e-01 9.595926e-106
## model_id model_method feats max.nTuningRuns
## 1 Random.myrandom_classfr myrandom_classfr .rnorm 0
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.252 0.001 0.4877665
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.4 0.6313559 0.4613003
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.4295557 0.4932808 0 0.5196257
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.6329502 0.4630045
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.4298903 0.4963638 0# Any models that have tuning parameters has "better" results with cross-validation
# (except rf) & "different" results for different outcome metrics
# Max.cor.Y
# Check impact of cv
# rpart is not a good candidate since caret does not optimize cp (only tuning parameter of rpart) well
ret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)## [1] "fitting model: Max.cor.Y.cv.0.rpart"
## [1] " indep_vars: biddable, startprice"## Loading required package: rpart## Fitting cp = 0.526 on full training set## Loading required package: rpart.plot
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 969
##
## CP nsplit rel error
## 1 0.5257271 0 1
##
## Node number 1: 969 observations
## predicted class=N expected loss=0.4613003 P(node) =1
## class counts: 522 447
## probabilities: 0.539 0.461
##
## n= 969
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 969 447 N (0.5386997 0.4613003) *
## [1] " calling mypredict_mdl for fit:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Max.cor.Y.cv.0.rpart.N
## 1 N 522
## 2 Y 447
## Prediction
## Reference N Y
## N 522 0
## Y 447 0
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5.386997e-01 0.000000e+00 5.067192e-01 5.704443e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 5.131824e-01 8.826336e-99
## [1] " calling mypredict_mdl for OOB:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Max.cor.Y.cv.0.rpart.N
## 1 N 479
## 2 Y 413
## Prediction
## Reference N Y
## N 479 0
## Y 413 0
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5.369955e-01 0.000000e+00 5.036362e-01 5.701097e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 5.137205e-01 2.217817e-91
## model_id model_method feats max.nTuningRuns
## 1 Max.cor.Y.cv.0.rpart rpart biddable, startprice 0
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.679 0.011 0.5
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.5 0 0.5386997
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.5067192 0.5704443 0 0.5
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.5 0 0.5369955
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.5036362 0.5701097 0ret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0.cp.0",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=0,
tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))## [1] "fitting model: Max.cor.Y.cv.0.cp.0.rpart"
## [1] " indep_vars: biddable, startprice"
## Fitting cp = 0 on full training set
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 969
##
## CP nsplit rel error
## 1 0.525727069 0 1.0000000
## 2 0.017897092 1 0.4742729
## 3 0.007270694 3 0.4384787
## 4 0.002237136 7 0.4093960
## 5 0.000000000 18 0.3847875
##
## Variable importance
## biddable startprice
## 51 49
##
## Node number 1: 969 observations, complexity param=0.5257271
## predicted class=N expected loss=0.4613003 P(node) =1
## class counts: 522 447
## probabilities: 0.539 0.461
## left son=2 (530 obs) right son=3 (439 obs)
## Primary splits:
## biddable < 0.5 to the left, improve=150.6565, (0 missing)
## startprice < 126.475 to the right, improve=127.7985, (0 missing)
## Surrogate splits:
## startprice < 152.995 to the right, agree=0.76, adj=0.469, (0 split)
##
## Node number 2: 530 observations, complexity param=0.002237136
## predicted class=N expected loss=0.2075472 P(node) =0.5469556
## class counts: 420 110
## probabilities: 0.792 0.208
## left son=4 (265 obs) right son=5 (265 obs)
## Primary splits:
## startprice < 261.995 to the right, improve=6.656604, (0 missing)
##
## Node number 3: 439 observations, complexity param=0.01789709
## predicted class=Y expected loss=0.2323462 P(node) =0.4530444
## class counts: 102 337
## probabilities: 0.232 0.768
## left son=6 (154 obs) right son=7 (285 obs)
## Primary splits:
## startprice < 127.5 to the right, improve=39.11474, (0 missing)
##
## Node number 4: 265 observations, complexity param=0.002237136
## predicted class=N expected loss=0.1283019 P(node) =0.2734778
## class counts: 231 34
## probabilities: 0.872 0.128
## left son=8 (18 obs) right son=9 (247 obs)
## Primary splits:
## startprice < 279.995 to the left, improve=0.6357956, (0 missing)
##
## Node number 5: 265 observations, complexity param=0.002237136
## predicted class=N expected loss=0.2867925 P(node) =0.2734778
## class counts: 189 76
## probabilities: 0.713 0.287
## left son=10 (216 obs) right son=11 (49 obs)
## Primary splits:
## startprice < 91 to the right, improve=2.416806, (0 missing)
##
## Node number 6: 154 observations, complexity param=0.01789709
## predicted class=N expected loss=0.4805195 P(node) =0.1589267
## class counts: 80 74
## probabilities: 0.519 0.481
## left son=12 (24 obs) right son=13 (130 obs)
## Primary splits:
## startprice < 414.995 to the right, improve=5.601066, (0 missing)
##
## Node number 7: 285 observations
## predicted class=Y expected loss=0.07719298 P(node) =0.2941176
## class counts: 22 263
## probabilities: 0.077 0.923
##
## Node number 8: 18 observations
## predicted class=N expected loss=0 P(node) =0.01857585
## class counts: 18 0
## probabilities: 1.000 0.000
##
## Node number 9: 247 observations, complexity param=0.002237136
## predicted class=N expected loss=0.1376518 P(node) =0.254902
## class counts: 213 34
## probabilities: 0.862 0.138
## left son=18 (196 obs) right son=19 (51 obs)
## Primary splits:
## startprice < 319.995 to the right, improve=1.22551, (0 missing)
##
## Node number 10: 216 observations
## predicted class=N expected loss=0.2546296 P(node) =0.2229102
## class counts: 161 55
## probabilities: 0.745 0.255
##
## Node number 11: 49 observations, complexity param=0.002237136
## predicted class=N expected loss=0.4285714 P(node) =0.0505676
## class counts: 28 21
## probabilities: 0.571 0.429
## left son=22 (9 obs) right son=23 (40 obs)
## Primary splits:
## startprice < 29.37 to the left, improve=0.9388889, (0 missing)
##
## Node number 12: 24 observations
## predicted class=N expected loss=0.1666667 P(node) =0.0247678
## class counts: 20 4
## probabilities: 0.833 0.167
##
## Node number 13: 130 observations, complexity param=0.007270694
## predicted class=Y expected loss=0.4615385 P(node) =0.1341589
## class counts: 60 70
## probabilities: 0.462 0.538
## left son=26 (123 obs) right son=27 (7 obs)
## Primary splits:
## startprice < 397 to the left, improve=0.4574288, (0 missing)
##
## Node number 18: 196 observations, complexity param=0.002237136
## predicted class=N expected loss=0.1122449 P(node) =0.2022704
## class counts: 174 22
## probabilities: 0.888 0.112
## left son=36 (87 obs) right son=37 (109 obs)
## Primary splits:
## startprice < 407.49 to the left, improve=0.5860584, (0 missing)
##
## Node number 19: 51 observations, complexity param=0.002237136
## predicted class=N expected loss=0.2352941 P(node) =0.05263158
## class counts: 39 12
## probabilities: 0.765 0.235
## left son=38 (44 obs) right son=39 (7 obs)
## Primary splits:
## startprice < 319.425 to the left, improve=1.833461, (0 missing)
##
## Node number 22: 9 observations
## predicted class=N expected loss=0.2222222 P(node) =0.009287926
## class counts: 7 2
## probabilities: 0.778 0.222
##
## Node number 23: 40 observations, complexity param=0.002237136
## predicted class=N expected loss=0.475 P(node) =0.04127967
## class counts: 21 19
## probabilities: 0.525 0.475
## left son=46 (23 obs) right son=47 (17 obs)
## Primary splits:
## startprice < 77.5 to the right, improve=0.7581841, (0 missing)
##
## Node number 26: 123 observations, complexity param=0.007270694
## predicted class=Y expected loss=0.4715447 P(node) =0.126935
## class counts: 58 65
## probabilities: 0.472 0.528
## left son=52 (22 obs) right son=53 (101 obs)
## Primary splits:
## startprice < 299.995 to the right, improve=0.7634593, (0 missing)
##
## Node number 27: 7 observations
## predicted class=Y expected loss=0.2857143 P(node) =0.007223942
## class counts: 2 5
## probabilities: 0.286 0.714
##
## Node number 36: 87 observations
## predicted class=N expected loss=0.06896552 P(node) =0.08978328
## class counts: 81 6
## probabilities: 0.931 0.069
##
## Node number 37: 109 observations, complexity param=0.002237136
## predicted class=N expected loss=0.146789 P(node) =0.1124871
## class counts: 93 16
## probabilities: 0.853 0.147
## left son=74 (102 obs) right son=75 (7 obs)
## Primary splits:
## startprice < 424.995 to the right, improve=7.549251, (0 missing)
##
## Node number 38: 44 observations
## predicted class=N expected loss=0.1818182 P(node) =0.04540764
## class counts: 36 8
## probabilities: 0.818 0.182
##
## Node number 39: 7 observations
## predicted class=Y expected loss=0.4285714 P(node) =0.007223942
## class counts: 3 4
## probabilities: 0.429 0.571
##
## Node number 46: 23 observations
## predicted class=N expected loss=0.3913043 P(node) =0.02373581
## class counts: 14 9
## probabilities: 0.609 0.391
##
## Node number 47: 17 observations
## predicted class=Y expected loss=0.4117647 P(node) =0.01754386
## class counts: 7 10
## probabilities: 0.412 0.588
##
## Node number 52: 22 observations
## predicted class=N expected loss=0.4090909 P(node) =0.02270382
## class counts: 13 9
## probabilities: 0.591 0.409
##
## Node number 53: 101 observations, complexity param=0.007270694
## predicted class=Y expected loss=0.4455446 P(node) =0.1042312
## class counts: 45 56
## probabilities: 0.446 0.554
## left son=106 (70 obs) right son=107 (31 obs)
## Primary splits:
## startprice < 244.98 to the left, improve=1.352603, (0 missing)
##
## Node number 74: 102 observations
## predicted class=N expected loss=0.09803922 P(node) =0.1052632
## class counts: 92 10
## probabilities: 0.902 0.098
##
## Node number 75: 7 observations
## predicted class=Y expected loss=0.1428571 P(node) =0.007223942
## class counts: 1 6
## probabilities: 0.143 0.857
##
## Node number 106: 70 observations, complexity param=0.007270694
## predicted class=N expected loss=0.5 P(node) =0.07223942
## class counts: 35 35
## probabilities: 0.500 0.500
## left son=212 (15 obs) right son=213 (55 obs)
## Primary splits:
## startprice < 199.995 to the right, improve=3.436364, (0 missing)
##
## Node number 107: 31 observations
## predicted class=Y expected loss=0.3225806 P(node) =0.03199174
## class counts: 10 21
## probabilities: 0.323 0.677
##
## Node number 212: 15 observations
## predicted class=N expected loss=0.2 P(node) =0.01547988
## class counts: 12 3
## probabilities: 0.800 0.200
##
## Node number 213: 55 observations, complexity param=0.002237136
## predicted class=Y expected loss=0.4181818 P(node) =0.05675955
## class counts: 23 32
## probabilities: 0.418 0.582
## left son=426 (31 obs) right son=427 (24 obs)
## Primary splits:
## startprice < 159.995 to the left, improve=1.363099, (0 missing)
##
## Node number 426: 31 observations, complexity param=0.002237136
## predicted class=N expected loss=0.483871 P(node) =0.03199174
## class counts: 16 15
## probabilities: 0.516 0.484
## left son=852 (8 obs) right son=853 (23 obs)
## Primary splits:
## startprice < 149.995 to the left, improve=0.2556101, (0 missing)
##
## Node number 427: 24 observations
## predicted class=Y expected loss=0.2916667 P(node) =0.0247678
## class counts: 7 17
## probabilities: 0.292 0.708
##
## Node number 852: 8 observations
## predicted class=N expected loss=0.375 P(node) =0.008255934
## class counts: 5 3
## probabilities: 0.625 0.375
##
## Node number 853: 23 observations
## predicted class=Y expected loss=0.4782609 P(node) =0.02373581
## class counts: 11 12
## probabilities: 0.478 0.522
##
## n= 969
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 969 447 N (0.53869969 0.46130031)
## 2) biddable< 0.5 530 110 N (0.79245283 0.20754717)
## 4) startprice>=261.995 265 34 N (0.87169811 0.12830189)
## 8) startprice< 279.995 18 0 N (1.00000000 0.00000000) *
## 9) startprice>=279.995 247 34 N (0.86234818 0.13765182)
## 18) startprice>=319.995 196 22 N (0.88775510 0.11224490)
## 36) startprice< 407.49 87 6 N (0.93103448 0.06896552) *
## 37) startprice>=407.49 109 16 N (0.85321101 0.14678899)
## 74) startprice>=424.995 102 10 N (0.90196078 0.09803922) *
## 75) startprice< 424.995 7 1 Y (0.14285714 0.85714286) *
## 19) startprice< 319.995 51 12 N (0.76470588 0.23529412)
## 38) startprice< 319.425 44 8 N (0.81818182 0.18181818) *
## 39) startprice>=319.425 7 3 Y (0.42857143 0.57142857) *
## 5) startprice< 261.995 265 76 N (0.71320755 0.28679245)
## 10) startprice>=91 216 55 N (0.74537037 0.25462963) *
## 11) startprice< 91 49 21 N (0.57142857 0.42857143)
## 22) startprice< 29.37 9 2 N (0.77777778 0.22222222) *
## 23) startprice>=29.37 40 19 N (0.52500000 0.47500000)
## 46) startprice>=77.5 23 9 N (0.60869565 0.39130435) *
## 47) startprice< 77.5 17 7 Y (0.41176471 0.58823529) *
## 3) biddable>=0.5 439 102 Y (0.23234624 0.76765376)
## 6) startprice>=127.5 154 74 N (0.51948052 0.48051948)
## 12) startprice>=414.995 24 4 N (0.83333333 0.16666667) *
## 13) startprice< 414.995 130 60 Y (0.46153846 0.53846154)
## 26) startprice< 397 123 58 Y (0.47154472 0.52845528)
## 52) startprice>=299.995 22 9 N (0.59090909 0.40909091) *
## 53) startprice< 299.995 101 45 Y (0.44554455 0.55445545)
## 106) startprice< 244.98 70 35 N (0.50000000 0.50000000)
## 212) startprice>=199.995 15 3 N (0.80000000 0.20000000) *
## 213) startprice< 199.995 55 23 Y (0.41818182 0.58181818)
## 426) startprice< 159.995 31 15 N (0.51612903 0.48387097)
## 852) startprice< 149.995 8 3 N (0.62500000 0.37500000) *
## 853) startprice>=149.995 23 11 Y (0.47826087 0.52173913) *
## 427) startprice>=159.995 24 7 Y (0.29166667 0.70833333) *
## 107) startprice>=244.98 31 10 Y (0.32258065 0.67741935) *
## 27) startprice>=397 7 2 Y (0.28571429 0.71428571) *
## 7) startprice< 127.5 285 22 Y (0.07719298 0.92280702) *
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.7129859
## 3 0.2 0.7344435
## 4 0.3 0.7968923
## 5 0.4 0.7977011
## 6 0.5 0.7971698
## 7 0.6 0.7790262
## 8 0.7 0.7558442
## 9 0.8 0.7280108
## 10 0.9 0.7185792
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.N
## 1 N 446
## 2 Y 100
## sold.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.Y
## 1 76
## 2 347
## Prediction
## Reference N Y
## N 446 76
## Y 100 347
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 8.183695e-01 6.331346e-01 7.926235e-01 8.421635e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 7.658838e-75 8.297306e-02
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6731449
## 3 0.2 0.6814815
## 4 0.3 0.7294982
## 5 0.4 0.7111682
## 6 0.5 0.6973684
## 7 0.6 0.6860304
## 8 0.7 0.6800000
## 9 0.8 0.6706587
## 10 0.9 0.6706949
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.N
## 1 N 373
## 2 Y 115
## sold.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.Y
## 1 106
## 2 298
## Prediction
## Reference N Y
## N 373 106
## Y 115 298
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.522422e-01 5.010074e-01 7.225457e-01 7.802619e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 3.066024e-40 5.904816e-01
## model_id model_method feats
## 1 Max.cor.Y.cv.0.cp.0.rpart rpart biddable, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 0 0.47 0.008
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8775832 0.4 0.7977011 0.8183695
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7926235 0.8421635 0.6331346 0.790888
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.3 0.7294982 0.7522422
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.7225457 0.7802619 0.5010074if (glb_is_regression || glb_is_binomial) # For multinomials this model will be run next by default
ret_lst <- myfit_mdl(model_id="Max.cor.Y",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Max.cor.Y.rpart"
## [1] " indep_vars: biddable, startprice"
## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.00727 on full training set## Warning in myfit_mdl(model_id = "Max.cor.Y", model_method = "rpart",
## model_type = glb_model_type, : model's bestTune found at an extreme of
## tuneGrid for parameter: cp
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 969
##
## CP nsplit rel error
## 1 0.525727069 0 1.0000000
## 2 0.017897092 1 0.4742729
## 3 0.007270694 3 0.4384787
##
## Variable importance
## biddable startprice
## 57 43
##
## Node number 1: 969 observations, complexity param=0.5257271
## predicted class=N expected loss=0.4613003 P(node) =1
## class counts: 522 447
## probabilities: 0.539 0.461
## left son=2 (530 obs) right son=3 (439 obs)
## Primary splits:
## biddable < 0.5 to the left, improve=150.6565, (0 missing)
## startprice < 126.475 to the right, improve=127.7985, (0 missing)
## Surrogate splits:
## startprice < 152.995 to the right, agree=0.76, adj=0.469, (0 split)
##
## Node number 2: 530 observations
## predicted class=N expected loss=0.2075472 P(node) =0.5469556
## class counts: 420 110
## probabilities: 0.792 0.208
##
## Node number 3: 439 observations, complexity param=0.01789709
## predicted class=Y expected loss=0.2323462 P(node) =0.4530444
## class counts: 102 337
## probabilities: 0.232 0.768
## left son=6 (154 obs) right son=7 (285 obs)
## Primary splits:
## startprice < 127.5 to the right, improve=39.11474, (0 missing)
##
## Node number 6: 154 observations, complexity param=0.01789709
## predicted class=N expected loss=0.4805195 P(node) =0.1589267
## class counts: 80 74
## probabilities: 0.519 0.481
## left son=12 (24 obs) right son=13 (130 obs)
## Primary splits:
## startprice < 414.995 to the right, improve=5.601066, (0 missing)
##
## Node number 7: 285 observations
## predicted class=Y expected loss=0.07719298 P(node) =0.2941176
## class counts: 22 263
## probabilities: 0.077 0.923
##
## Node number 12: 24 observations
## predicted class=N expected loss=0.1666667 P(node) =0.0247678
## class counts: 20 4
## probabilities: 0.833 0.167
##
## Node number 13: 130 observations
## predicted class=Y expected loss=0.4615385 P(node) =0.1341589
## class counts: 60 70
## probabilities: 0.462 0.538
##
## n= 969
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 969 447 N (0.53869969 0.46130031)
## 2) biddable< 0.5 530 110 N (0.79245283 0.20754717) *
## 3) biddable>=0.5 439 102 Y (0.23234624 0.76765376)
## 6) startprice>=127.5 154 74 N (0.51948052 0.48051948)
## 12) startprice>=414.995 24 4 N (0.83333333 0.16666667) *
## 13) startprice< 414.995 130 60 Y (0.46153846 0.53846154) *
## 7) startprice< 127.5 285 22 Y (0.07719298 0.92280702) *
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.6313559
## 3 0.2 0.6364943
## 4 0.3 0.7726218
## 5 0.4 0.7726218
## 6 0.5 0.7726218
## 7 0.6 0.7185792
## 8 0.7 0.7185792
## 9 0.8 0.7185792
## 10 0.9 0.7185792
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Max.cor.Y.rpart.N
## 1 N 440
## 2 Y 114
## sold.fctr.predict.Max.cor.Y.rpart.Y
## 1 82
## 2 333
## Prediction
## Reference N Y
## N 440 82
## Y 114 333
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.977296e-01 5.909173e-01 7.710339e-01 8.226019e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 1.071676e-63 2.680913e-02
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6329502
## 3 0.2 0.6320682
## 4 0.3 0.7478043
## 5 0.4 0.7478043
## 6 0.5 0.7478043
## 7 0.6 0.6706949
## 8 0.7 0.6706949
## 9 0.8 0.6706949
## 10 0.9 0.6706949
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Max.cor.Y.rpart.N
## 1 N 393
## 2 Y 115
## sold.fctr.predict.Max.cor.Y.rpart.Y
## 1 86
## 2 298
## Prediction
## Reference N Y
## N 393 86
## Y 115 298
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.746637e-01 5.446437e-01 7.458018e-01 8.016983e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 3.787245e-49 4.827181e-02
## model_id model_method feats max.nTuningRuns
## 1 Max.cor.Y.rpart rpart biddable, startprice 3
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.949 0.011 0.8255676
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.5 0.7726218 0.7894737
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7710339 0.8226019 0.571941 0.7965723
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.5 0.7478043 0.7746637
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.7458018 0.8016983 0.5446437
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.009287926 0.01597718# Used to compare vs. Interactions.High.cor.Y and/or Max.cor.Y.TmSrs
ret_lst <- myfit_mdl(model_id="Max.cor.Y",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Max.cor.Y.glm"
## [1] " indep_vars: biddable, startprice"
## Aggregating results
## Fitting final model on full training set
##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.0828 -0.7376 -0.2970 0.6044 2.7762
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.1277322 0.1758847 0.726 0.468
## biddable 1.9492275 0.1698126 11.479 <2e-16 ***
## startprice -0.0058665 0.0006211 -9.446 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1337.51 on 968 degrees of freedom
## Residual deviance: 906.51 on 966 degrees of freedom
## AIC: 912.51
##
## Number of Fisher Scoring iterations: 5
##
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.6697747
## 3 0.2 0.7204207
## 4 0.3 0.7479839
## 5 0.4 0.7771679
## 6 0.5 0.7636787
## 7 0.6 0.7602906
## 8 0.7 0.7484197
## 9 0.8 0.6990291
## 10 0.9 0.0000000
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Max.cor.Y.glm.N
## 1 N 412
## 2 Y 93
## sold.fctr.predict.Max.cor.Y.glm.Y
## 1 110
## 2 354
## Prediction
## Reference N Y
## N 412 110
## Y 93 354
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.905057e-01 5.796347e-01 7.635025e-01 8.157303e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 4.625452e-60 2.614461e-01
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6628099
## 3 0.2 0.6883721
## 4 0.3 0.7178947
## 5 0.4 0.7408284
## 6 0.5 0.7427854
## 7 0.6 0.7291667
## 8 0.7 0.7317073
## 9 0.8 0.6615385
## 10 0.9 0.0000000
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Max.cor.Y.glm.N
## 1 N 391
## 2 Y 117
## sold.fctr.predict.Max.cor.Y.glm.Y
## 1 88
## 2 296
## Prediction
## Reference N Y
## N 391 88
## Y 117 296
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.701794e-01 5.355819e-01 7.411419e-01 7.974197e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 2.794959e-47 5.051172e-02
## model_id model_method feats max.nTuningRuns
## 1 Max.cor.Y.glm glm biddable, startprice 1
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.923 0.011 0.8592854
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.4 0.7771679 0.7915377
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7635025 0.8157303 0.5781217 0.8223119
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.5 0.7427854 0.7701794
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1 0.7411419 0.7974197 0.5355819 912.5107
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.01251223 0.02532251if (!is.null(glb_date_vars) &&
(sum(grepl(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
names(glb_allobs_df))) > 0)) {
# ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly1",
# model_method=ifelse(glb_is_regression, "lm",
# ifelse(glb_is_binomial, "glm", "rpart")),
# model_type=glb_model_type,
# indep_vars_vctr=c(max_cor_y_x_vars, paste0(glb_date_vars, ".day.minutes")),
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
#
ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr=c(max_cor_y_x_vars,
grep(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
names(glb_allobs_df), value=TRUE)),
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
}
# Interactions.High.cor.Y
if (length(int_feats <- setdiff(unique(glb_feats_df$cor.high.X), NA)) > 0) {
# lm & glm handle interaction terms; rpart & rf do not
if (glb_is_regression || glb_is_binomial) {
indep_vars_vctr <-
c(max_cor_y_x_vars, paste(max_cor_y_x_vars[1], int_feats, sep=":"))
} else { indep_vars_vctr <- union(max_cor_y_x_vars, int_feats) }
ret_lst <- myfit_mdl(model_id="Interact.High.cor.Y",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr,
glb_rsp_var, glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
} ## [1] "fitting model: Interact.High.cor.Y.glm"
## [1] " indep_vars: biddable, startprice, biddable:D.nwrds.unq.log, biddable:D.T.like, biddable:D.npnct06.log, biddable:D.ratio.nstopwrds.nwrds, biddable:D.nchrs.log, biddable:D.nwrds.log, biddable:cellular.fctr"
## Aggregating results
## Fitting final model on full training set
##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.1656 -0.7374 -0.2899 0.6201 2.8003
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.1603089 0.1781228 0.900 0.3681
## biddable 1.6190963 2.8770894 0.563 0.5736
## startprice -0.0060165 0.0006372 -9.443 <2e-16
## `biddable:D.nwrds.unq.log` 0.3826251 1.8998454 0.201 0.8404
## `biddable:D.T.like` -0.6314219 0.7342195 -0.860 0.3898
## `biddable:D.npnct06.log` 0.6709083 1.0923018 0.614 0.5391
## `biddable:D.ratio.nstopwrds.nwrds` 0.3675223 2.8732634 0.128 0.8982
## `biddable:D.nchrs.log` 1.0243780 1.3863636 0.739 0.4600
## `biddable:D.nwrds.log` -1.9438664 2.6476493 -0.734 0.4628
## `biddable:cellular.fctr1` 0.3094437 0.3105257 0.997 0.3190
## `biddable:cellular.fctrUnknown` -0.8380709 0.3768660 -2.224 0.0262
##
## (Intercept)
## biddable
## startprice ***
## `biddable:D.nwrds.unq.log`
## `biddable:D.T.like`
## `biddable:D.npnct06.log`
## `biddable:D.ratio.nstopwrds.nwrds`
## `biddable:D.nchrs.log`
## `biddable:D.nwrds.log`
## `biddable:cellular.fctr1`
## `biddable:cellular.fctrUnknown` *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1337.51 on 968 degrees of freedom
## Residual deviance: 896.27 on 958 degrees of freedom
## AIC: 918.27
##
## Number of Fisher Scoring iterations: 5
##
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.6708171
## 3 0.2 0.7210526
## 4 0.3 0.7489960
## 5 0.4 0.7753304
## 6 0.5 0.7654609
## 7 0.6 0.7585366
## 8 0.7 0.7560664
## 9 0.8 0.6798867
## 10 0.9 0.2111554
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Interact.High.cor.Y.glm.N
## 1 N 413
## 2 Y 95
## sold.fctr.predict.Interact.High.cor.Y.glm.Y
## 1 109
## 2 352
## Prediction
## Reference N Y
## N 413 109
## Y 95 352
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.894737e-01 5.773607e-01 7.624276e-01 8.147476e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 1.491405e-59 3.627265e-01
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6639004
## 3 0.2 0.6902985
## 4 0.3 0.7178947
## 5 0.4 0.7434679
## 6 0.5 0.7424242
## 7 0.6 0.7279895
## 8 0.7 0.7213115
## 9 0.8 0.6342229
## 10 0.9 0.2073434
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Interact.High.cor.Y.glm.N
## 1 N 363
## 2 Y 100
## sold.fctr.predict.Interact.High.cor.Y.glm.Y
## 1 116
## 2 313
## Prediction
## Reference N Y
## N 363 116
## Y 100 313
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.578475e-01 5.143253e-01 7.283498e-01 7.856310e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 2.288444e-42 3.074342e-01
## model_id model_method
## 1 Interact.High.cor.Y.glm glm
## feats
## 1 biddable, startprice, biddable:D.nwrds.unq.log, biddable:D.T.like, biddable:D.npnct06.log, biddable:D.ratio.nstopwrds.nwrds, biddable:D.nchrs.log, biddable:D.nwrds.log, biddable:cellular.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 0.941 0.015
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8593261 0.4 0.7753304 0.7894737
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7624276 0.8147476 0.5739487 0.8220844
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.7434679 0.7578475
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1 0.7283498 0.785631 0.5143253 918.2717
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.008191181 0.01641682# Low.cor.X
# if (glb_is_classification && glb_is_binomial)
# indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) &
# is.ConditionalX.y &
# (exclude.as.feat != 1))[, "id"] else
indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) & !myNearZV &
(exclude.as.feat != 1))[, "id"]
myadjust_interaction_feats <- function(vars_vctr) {
for (feat in subset(glb_feats_df, !is.na(interaction.feat))$id)
if (feat %in% vars_vctr)
vars_vctr <- union(setdiff(vars_vctr, feat),
paste0(glb_feats_df[glb_feats_df$id == feat, "interaction.feat"], ":", feat))
return(vars_vctr)
}
indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)
ret_lst <- myfit_mdl(model_id="Low.cor.X",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
indep_vars_vctr=indep_vars_vctr,
model_type=glb_model_type,
glb_rsp_var, glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Low.cor.X.glm"
## [1] " indep_vars: biddable, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.npnct08.log, D.T.condit, color.fctr, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.4494 -0.6476 -0.1489 0.5762 3.7614
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error z value
## (Intercept) 0.549285 0.747141 0.735
## biddable 1.669934 0.203447 8.208
## D.npnct15.log 1.634624 1.074840 1.521
## D.T.screen -0.500128 0.756696 -0.661
## D.npnct03.log 0.261222 1.364464 0.191
## D.T.used 0.007099 0.600843 0.012
## D.T.excellent 0.266740 0.399992 0.667
## D.T.great 0.132775 0.587850 0.226
## D.ratio.sum.TfIdf.nwrds 0.027812 0.276785 0.100
## D.T.good -0.069589 0.607954 -0.114
## D.npnct01.log -0.907332 0.849304 -1.068
## D.T.veri 0.099823 0.816962 0.122
## D.T.work 0.376708 0.739715 0.509
## D.T.scratch 0.393439 0.719887 0.547
## D.P.air -1.462526 1.047010 -1.397
## D.T.use 0.475565 0.853770 0.557
## storage.fctr16 -0.394703 0.635061 -0.622
## storage.fctr32 0.019785 0.648333 0.031
## storage.fctr64 0.144251 0.637235 0.226
## storage.fctrUnknown 0.801171 0.811666 0.987
## D.P.mini 0.489395 0.896087 0.546
## D.T.condition 0.517055 0.847573 0.610
## D.npnct11.log 0.366762 0.334335 1.097
## .rnorm -0.134883 0.096995 -1.391
## D.T.ipad 0.285937 0.915310 0.312
## D.npnct10.log 0.129428 1.660022 0.078
## D.npnct08.log -0.460183 0.709655 -0.648
## D.T.condit 0.249940 0.524936 0.476
## color.fctrBlack 0.223018 0.251124 0.888
## color.fctrGold 0.168227 0.609980 0.276
## `color.fctrSpace Gray` 0.151872 0.340833 0.446
## color.fctrWhite 0.319402 0.253428 1.260
## D.T.this 0.518550 1.050050 0.494
## D.npnct06.log -0.803564 0.912236 -0.881
## D.T.box -0.108414 0.842232 -0.129
## D.npnct28.log -1.997913 932.426720 -0.002
## D.T.like 0.069369 0.494053 0.140
## D.npnct12.log -1.037034 0.758094 -1.368
## D.npnct09.log -8.402339 557.713545 -0.015
## D.nwrds.unq.log -0.201648 0.163667 -1.232
## D.ndgts.log 0.470754 0.421324 1.117
## cellular.fctr1 0.378635 0.222719 1.700
## cellular.fctrUnknown -0.265270 0.517793 -0.512
## D.npnct14.log 0.090695 0.828304 0.109
## `prdline.my.fctriPad 2` 0.598130 0.345694 1.730
## `prdline.my.fctriPad 3` 1.037743 0.389782 2.662
## `prdline.my.fctriPad 4` 0.914501 0.450335 2.031
## `prdline.my.fctriPad 5` NA NA NA
## `prdline.my.fctriPad Air` 1.631788 0.486359 3.355
## `prdline.my.fctriPad Air 2` 3.085394 0.596495 5.173
## `prdline.my.fctriPad mini` 0.557883 0.350809 1.590
## `prdline.my.fctriPad mini 2` 1.591777 0.533071 2.986
## `prdline.my.fctriPad mini 3` 0.705251 0.754143 0.935
## `prdline.my.fctriPad mini Retina` 2.209463 1.039294 2.126
## prdline.my.fctrUnknown -0.524367 0.478375 -1.096
## D.npnct05.log -2.199460 1.634299 -1.346
## `condition.fctrFor parts or not working` -0.893925 0.344079 -2.598
## `condition.fctrManufacturer refurbished` 0.664466 0.783604 0.848
## condition.fctrNew -0.178644 0.347314 -0.514
## `condition.fctrNew other (see details)` 0.030578 0.488619 0.063
## `condition.fctrSeller refurbished` -0.891650 0.435204 -2.049
## startprice -0.011123 0.001279 -8.696
## Pr(>|z|)
## (Intercept) 0.462228
## biddable 2.25e-16 ***
## D.npnct15.log 0.128308
## D.T.screen 0.508653
## D.npnct03.log 0.848176
## D.T.used 0.990574
## D.T.excellent 0.504859
## D.T.great 0.821306
## D.ratio.sum.TfIdf.nwrds 0.919963
## D.T.good 0.908869
## D.npnct01.log 0.285375
## D.T.veri 0.902750
## D.T.work 0.610569
## D.T.scratch 0.584702
## D.P.air 0.162456
## D.T.use 0.577516
## storage.fctr16 0.534258
## storage.fctr32 0.975655
## storage.fctr64 0.820914
## storage.fctrUnknown 0.323609
## D.P.mini 0.584965
## D.T.condition 0.541834
## D.npnct11.log 0.272646
## .rnorm 0.164342
## D.T.ipad 0.754741
## D.npnct10.log 0.937854
## D.npnct08.log 0.516688
## D.T.condit 0.633979
## color.fctrBlack 0.374498
## color.fctrGold 0.782708
## `color.fctrSpace Gray` 0.655893
## color.fctrWhite 0.207552
## D.T.this 0.621424
## D.npnct06.log 0.378386
## D.T.box 0.897577
## D.npnct28.log 0.998290
## D.T.like 0.888338
## D.npnct12.log 0.171328
## D.npnct09.log 0.987980
## D.nwrds.unq.log 0.217927
## D.ndgts.log 0.263857
## cellular.fctr1 0.089121 .
## cellular.fctrUnknown 0.608434
## D.npnct14.log 0.912810
## `prdline.my.fctriPad 2` 0.083589 .
## `prdline.my.fctriPad 3` 0.007759 **
## `prdline.my.fctriPad 4` 0.042284 *
## `prdline.my.fctriPad 5` NA
## `prdline.my.fctriPad Air` 0.000793 ***
## `prdline.my.fctriPad Air 2` 2.31e-07 ***
## `prdline.my.fctriPad mini` 0.111772
## `prdline.my.fctriPad mini 2` 0.002826 **
## `prdline.my.fctriPad mini 3` 0.349701
## `prdline.my.fctriPad mini Retina` 0.033509 *
## prdline.my.fctrUnknown 0.273016
## D.npnct05.log 0.178363
## `condition.fctrFor parts or not working` 0.009376 **
## `condition.fctrManufacturer refurbished` 0.396459
## condition.fctrNew 0.607001
## `condition.fctrNew other (see details)` 0.950100
## `condition.fctrSeller refurbished` 0.040481 *
## startprice < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1337.51 on 968 degrees of freedom
## Residual deviance: 812.64 on 908 degrees of freedom
## AIC: 934.64
##
## Number of Fisher Scoring iterations: 14
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.7116166
## 3 0.2 0.7572993
## 4 0.3 0.7700000
## 5 0.4 0.7813853
## 6 0.5 0.7954023
## 7 0.6 0.7918171
## 8 0.7 0.7662835
## 9 0.8 0.6966292
## 10 0.9 0.4501718
## 11 1.0 0.0000000## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Low.cor.X.glm.N
## 1 N 445
## 2 Y 101
## sold.fctr.predict.Low.cor.X.glm.Y
## 1 77
## 2 346
## Prediction
## Reference N Y
## N 445 77
## Y 101 346
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 8.163055e-01 6.289656e-01 7.904595e-01 8.402123e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 1.124987e-73 8.472177e-02
## [1] " calling mypredict_mdl for OOB:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6806283
## 3 0.2 0.6951456
## 4 0.3 0.7245119
## 5 0.4 0.7418605
## 6 0.5 0.7405542
## 7 0.6 0.7413333
## 8 0.7 0.7011494
## 9 0.8 0.6248038
## 10 0.9 0.3877159
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.Low.cor.X.glm.N
## 1 N 351
## 2 Y 94
## sold.fctr.predict.Low.cor.X.glm.Y
## 1 128
## 2 319
## Prediction
## Reference N Y
## N 351 128
## Y 94 319
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.511211e-01 5.023247e-01 7.213857e-01 7.791873e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 8.019721e-40 2.677277e-02
## model_id model_method
## 1 Low.cor.X.glm glm
## feats
## 1 biddable, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.npnct08.log, D.T.condit, color.fctr, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 1.235 0.129
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8890475 0.5 0.7954023 0.7636739
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7904595 0.8402123 0.5225041 0.8242202
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.7418605 0.7511211
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1 0.7213857 0.7791873 0.5023247 934.642
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.0170513 0.03600209rm(ret_lst)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 10 fit.models 7 0 41.384 65.926 24.542
## 11 fit.models 7 1 65.927 NA NAfit.models_1_chunk_df <- myadd_chunk(NULL, "fit.models_1_bgn")## label step_major step_minor bgn end elapsed
## 1 fit.models_1_bgn 1 0 70.29 NA NA# Options:
# 1. rpart & rf manual tuning
# 2. rf without pca (default: with pca)
#stop(here"); sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df
#glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df
# All X that is not user excluded
# if (glb_is_classification && glb_is_binomial) {
# model_id_pfx <- "Conditional.X"
# # indep_vars_vctr <- setdiff(names(glb_fitobs_df), union(glb_rsp_var, glb_exclude_vars_as_features))
# indep_vars_vctr <- subset(glb_feats_df, is.ConditionalX.y &
# (exclude.as.feat != 1))[, "id"]
# } else {
model_id_pfx <- "All.X"
indep_vars_vctr <- subset(glb_feats_df, !myNearZV &
(exclude.as.feat != 1))[, "id"]
# }
indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)
for (method in glb_models_method_vctr) {
fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df,
paste0("fit.models_1_", method), major.inc=TRUE)
if (method %in% c("rpart", "rf")) {
# rpart: fubar's the tree
# rf: skip the scenario w/ .rnorm for speed
indep_vars_vctr <- setdiff(indep_vars_vctr, c(".rnorm"))
model_id <- paste0(model_id_pfx, ".no.rnorm")
} else model_id <- model_id_pfx
ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
indep_vars_vctr=indep_vars_vctr,
model_type=glb_model_type,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
# If All.X.glm is less accurate than Low.Cor.X.glm
# check NA coefficients & filter appropriate terms in indep_vars_vctr
# if (method == "glm") {
# orig_glm <- glb_models_lst[[paste0(model_id, ".", model_method)]]$finalModel
# orig_glm <- glb_models_lst[["All.X.glm"]]$finalModel; print(summary(orig_glm))
# vif_orig_glm <- vif(orig_glm); print(vif_orig_glm)
# print(vif_orig_glm[!is.na(vif_orig_glm) & (vif_orig_glm == Inf)])
# print(which.max(vif_orig_glm))
# print(sort(vif_orig_glm[vif_orig_glm >= 1.0e+03], decreasing=TRUE))
# glb_fitobs_df[c(1143, 3637, 3953, 4105), c("UniqueID", "Popular", "H.P.quandary", "Headline")]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE), ]
# all.equal(glb_allobs_df$S.nuppr.log, glb_allobs_df$A.nuppr.log)
# all.equal(glb_allobs_df$S.npnct19.log, glb_allobs_df$A.npnct19.log)
# all.equal(glb_allobs_df$S.P.year.colon, glb_allobs_df$A.P.year.colon)
# all.equal(glb_allobs_df$S.T.share, glb_allobs_df$A.T.share)
# all.equal(glb_allobs_df$H.T.clip, glb_allobs_df$H.P.daily.clip.report)
# cor(glb_allobs_df$S.T.herald, glb_allobs_df$S.T.tribun)
# dsp_obs(Abstract.contains="[Dd]iar", cols=("Abstract"), all=TRUE)
# dsp_obs(Abstract.contains="[Ss]hare", cols=("Abstract"), all=TRUE)
# subset(glb_feats_df, cor.y.abs <= glb_feats_df[glb_feats_df$id == ".rnorm", "cor.y.abs"])
# corxx_mtrx <- cor(data.matrix(glb_allobs_df[, setdiff(names(glb_allobs_df), myfind_chr_cols_df(glb_allobs_df))]), use="pairwise.complete.obs"); abs_corxx_mtrx <- abs(corxx_mtrx); diag(abs_corxx_mtrx) <- 0
# which.max(abs_corxx_mtrx["S.T.tribun", ])
# abs_corxx_mtrx["A.npnct08.log", "S.npnct08.log"]
# step_glm <- step(orig_glm)
# }
# Since caret does not optimize rpart well
# if (method == "rpart")
# ret_lst <- myfit_mdl(model_id=paste0(model_id_pfx, ".cp.0"), model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# model_type=glb_model_type,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=0, tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))
}## label step_major step_minor bgn end elapsed
## 1 fit.models_1_bgn 1 0 70.290 70.309 0.019
## 2 fit.models_1_glm 2 0 70.309 NA NA
## [1] "fitting model: All.X.glm"
## [1] " indep_vars: biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice"
## Aggregating results
## Fitting final model on full training set## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.4666 -0.6341 -0.1250 0.5651 3.8127
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error z value
## (Intercept) 1.065e+01 5.802e+00 1.837
## biddable 1.679e+00 2.100e-01 7.993
## D.ratio.nstopwrds.nwrds -1.011e+01 5.789e+00 -1.746
## D.npnct15.log 1.600e+00 1.177e+00 1.359
## D.T.screen -6.056e-01 8.352e-01 -0.725
## D.npnct03.log -1.693e+00 1.829e+00 -0.926
## D.T.used -1.834e-01 8.613e-01 -0.213
## D.T.excellent 6.418e-01 4.014e-01 1.599
## D.T.great 4.107e-02 6.617e-01 0.062
## D.ratio.sum.TfIdf.nwrds -9.351e-01 6.160e-01 -1.518
## D.T.good -2.419e-01 7.465e-01 -0.324
## D.npnct01.log -1.212e+00 1.002e+00 -1.210
## D.T.veri 3.086e-01 8.772e-01 0.352
## D.T.work 6.618e-01 8.315e-01 0.796
## D.T.scratch 6.427e-01 8.525e-01 0.754
## D.P.air -1.265e+00 1.100e+00 -1.150
## D.T.use 7.229e-02 1.024e+00 0.071
## storage.fctr16 -3.407e-01 6.596e-01 -0.516
## storage.fctr32 4.736e-02 6.736e-01 0.070
## storage.fctr64 1.249e-01 6.625e-01 0.189
## storage.fctrUnknown 8.773e-01 8.466e-01 1.036
## D.P.mini 9.960e-01 1.098e+00 0.907
## D.T.condition 7.379e-01 1.084e+00 0.681
## D.npnct11.log 7.982e-01 4.323e-01 1.847
## .rnorm -1.239e-01 9.986e-02 -1.240
## D.T.ipad 4.921e-01 9.949e-01 0.495
## D.npnct10.log 1.751e+00 2.028e+00 0.863
## D.sum.TfIdf 2.251e-01 2.013e-01 1.118
## D.T.new 1.575e+00 1.026e+00 1.535
## D.npnct13.log -6.606e-02 4.957e-01 -0.133
## D.npnct08.log -2.172e-01 8.343e-01 -0.260
## D.T.condit 2.459e-01 6.708e-01 0.367
## color.fctrBlack 2.146e-01 2.600e-01 0.825
## color.fctrGold 6.885e-02 6.350e-01 0.108
## `color.fctrSpace Gray` 2.357e-01 3.494e-01 0.675
## color.fctrWhite 3.921e-01 2.612e-01 1.501
## D.nstopwrds.log 3.009e+00 1.773e+00 1.697
## D.npnct16.log 4.344e+00 2.120e+00 2.049
## D.npnct24.log 1.091e+01 8.304e+00 1.314
## D.T.this 4.128e-01 1.249e+00 0.330
## D.npnct06.log -4.102e+00 2.351e+00 -1.745
## D.T.box -1.419e+00 9.557e-01 -1.484
## D.npnct28.log -2.084e+00 8.629e+02 -0.002
## D.T.like -1.600e+00 8.986e-01 -1.781
## D.npnct12.log -3.745e-01 9.023e-01 -0.415
## D.nuppr.log 8.814e+00 8.405e+00 1.049
## D.nchrs.log -1.409e+01 9.870e+00 -1.428
## D.nwrds.log 2.959e+00 3.279e+00 0.902
## D.npnct09.log -7.681e+00 4.612e+02 -0.017
## D.nwrds.unq.log -1.421e+00 8.731e-01 -1.628
## D.ndgts.log 7.992e-01 6.724e-01 1.188
## `carrier.fctrAT&T` 1.489e+01 9.781e+02 0.015
## carrier.fctrOther 2.758e+01 1.382e+03 0.020
## carrier.fctrSprint 1.458e+01 9.781e+02 0.015
## `carrier.fctrT-Mobile` 1.396e+01 9.781e+02 0.014
## carrier.fctrUnknown 1.509e+01 9.781e+02 0.015
## carrier.fctrVerizon 1.500e+01 9.781e+02 0.015
## cellular.fctr1 -1.446e+01 9.781e+02 -0.015
## cellular.fctrUnknown -1.522e+01 9.781e+02 -0.016
## D.npnct14.log -4.078e-01 9.203e-01 -0.443
## `prdline.my.fctriPad 2` 5.687e-01 3.572e-01 1.592
## `prdline.my.fctriPad 3` 1.182e+00 4.117e-01 2.872
## `prdline.my.fctriPad 4` 8.142e-01 4.693e-01 1.735
## `prdline.my.fctriPad 5` NA NA NA
## `prdline.my.fctriPad Air` 1.723e+00 5.111e-01 3.370
## `prdline.my.fctriPad Air 2` 3.338e+00 6.215e-01 5.370
## `prdline.my.fctriPad mini` 5.317e-01 3.649e-01 1.457
## `prdline.my.fctriPad mini 2` 1.662e+00 5.522e-01 3.010
## `prdline.my.fctriPad mini 3` 8.264e-01 7.708e-01 1.072
## `prdline.my.fctriPad mini Retina` 2.286e+00 1.081e+00 2.114
## prdline.my.fctrUnknown -6.261e-01 5.045e-01 -1.241
## D.npnct05.log -2.387e+00 1.896e+00 -1.259
## `condition.fctrFor parts or not working` -1.094e+00 3.567e-01 -3.067
## `condition.fctrManufacturer refurbished` 6.024e-01 8.302e-01 0.726
## condition.fctrNew -2.202e-01 3.581e-01 -0.615
## `condition.fctrNew other (see details)` -1.446e-01 5.326e-01 -0.272
## `condition.fctrSeller refurbished` -7.365e-01 4.484e-01 -1.642
## startprice -1.166e-02 1.337e-03 -8.719
## Pr(>|z|)
## (Intercept) 0.066283 .
## biddable 1.32e-15 ***
## D.ratio.nstopwrds.nwrds 0.080731 .
## D.npnct15.log 0.174131
## D.T.screen 0.468389
## D.npnct03.log 0.354564
## D.T.used 0.831352
## D.T.excellent 0.109819
## D.T.great 0.950508
## D.ratio.sum.TfIdf.nwrds 0.129001
## D.T.good 0.745908
## D.npnct01.log 0.226451
## D.T.veri 0.724968
## D.T.work 0.426081
## D.T.scratch 0.450882
## D.P.air 0.250113
## D.T.use 0.943746
## storage.fctr16 0.605527
## storage.fctr32 0.943945
## storage.fctr64 0.850440
## storage.fctrUnknown 0.300107
## D.P.mini 0.364487
## D.T.condition 0.496018
## D.npnct11.log 0.064807 .
## .rnorm 0.214880
## D.T.ipad 0.620895
## D.npnct10.log 0.388027
## D.sum.TfIdf 0.263396
## D.T.new 0.124822
## D.npnct13.log 0.893978
## D.npnct08.log 0.794621
## D.T.condit 0.713954
## color.fctrBlack 0.409094
## color.fctrGold 0.913670
## `color.fctrSpace Gray` 0.499833
## color.fctrWhite 0.133235
## D.nstopwrds.log 0.089641 .
## D.npnct16.log 0.040456 *
## D.npnct24.log 0.188765
## D.T.this 0.741071
## D.npnct06.log 0.080979 .
## D.T.box 0.137738
## D.npnct28.log 0.998073
## D.T.like 0.074960 .
## D.npnct12.log 0.678073
## D.nuppr.log 0.294354
## D.nchrs.log 0.153332
## D.nwrds.log 0.366823
## D.npnct09.log 0.986712
## D.nwrds.unq.log 0.103520
## D.ndgts.log 0.234646
## `carrier.fctrAT&T` 0.987852
## carrier.fctrOther 0.984075
## carrier.fctrSprint 0.988107
## `carrier.fctrT-Mobile` 0.988611
## carrier.fctrUnknown 0.987688
## carrier.fctrVerizon 0.987767
## cellular.fctr1 0.988201
## cellular.fctrUnknown 0.987587
## D.npnct14.log 0.657695
## `prdline.my.fctriPad 2` 0.111324
## `prdline.my.fctriPad 3` 0.004083 **
## `prdline.my.fctriPad 4` 0.082751 .
## `prdline.my.fctriPad 5` NA
## `prdline.my.fctriPad Air` 0.000751 ***
## `prdline.my.fctriPad Air 2` 7.87e-08 ***
## `prdline.my.fctriPad mini` 0.145067
## `prdline.my.fctriPad mini 2` 0.002612 **
## `prdline.my.fctriPad mini 3` 0.283672
## `prdline.my.fctriPad mini Retina` 0.034533 *
## prdline.my.fctrUnknown 0.214562
## D.npnct05.log 0.208139
## `condition.fctrFor parts or not working` 0.002165 **
## `condition.fctrManufacturer refurbished` 0.468025
## condition.fctrNew 0.538508
## `condition.fctrNew other (see details)` 0.785948
## `condition.fctrSeller refurbished` 0.100488
## startprice < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1337.51 on 968 degrees of freedom
## Residual deviance: 785.15 on 892 degrees of freedom
## AIC: 939.15
##
## Number of Fisher Scoring iterations: 14
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.7205276
## 3 0.2 0.7673993
## 4 0.3 0.7871486
## 5 0.4 0.7961165
## 6 0.5 0.8009153
## 7 0.6 0.7913148
## 8 0.7 0.7770701
## 9 0.8 0.7138889
## 10 0.9 0.4991681
## 11 1.0 0.0000000## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.All.X.glm.N sold.fctr.predict.All.X.glm.Y
## 1 N 445 77
## 2 Y 97 350
## Prediction
## Reference N Y
## N 445 77
## Y 97 350
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 8.204334e-01 6.375374e-01 7.947886e-01 8.441134e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 5.071854e-76 1.497581e-01
## [1] " calling mypredict_mdl for OOB:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6838825
## 3 0.2 0.6961652
## 4 0.3 0.7142857
## 5 0.4 0.7374562
## 6 0.5 0.7315855
## 7 0.6 0.7267905
## 8 0.7 0.7188811
## 9 0.8 0.6296296
## 10 0.9 0.4149533
## 11 1.0 0.0000000## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.All.X.glm.N sold.fctr.predict.All.X.glm.Y
## 1 N 351 128
## 2 Y 97 316
## Prediction
## Reference N Y
## N 351 128
## Y 97 316
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.477578e-01 4.953483e-01 7.179071e-01 7.759620e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 1.384866e-38 4.550026e-02
## model_id model_method
## 1 All.X.glm glm
## feats
## 1 biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 1.366 0.176
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8974946 0.5 0.8009153 0.7574819
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7947886 0.8441134 0.5103726 0.8156723
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.7374562 0.7477578
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1 0.7179071 0.775962 0.4953483 939.1513
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.02876648 0.06032482
## label step_major step_minor bgn end elapsed
## 2 fit.models_1_glm 2 0 70.309 75.369 5.06
## 3 fit.models_1_bayesglm 3 0 75.369 NA NA
## [1] "fitting model: All.X.bayesglm"
## [1] " indep_vars: biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice"## Loading required package: arm
## Loading required package: MASS
##
## Attaching package: 'MASS'
##
## The following object is masked from 'package:dplyr':
##
## select
##
## Loading required package: Matrix
## Loading required package: lme4
##
## arm (Version 1.8-6, built: 2015-7-7)
##
## Working directory is /Users/bbalaji-2012/Documents/Work/Courses/MIT/Analytics_Edge_15_071x/Assignments/Kaggle_eBay_iPads
## Aggregating results
## Fitting final model on full training set
##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.3838 -0.6489 -0.1475 0.5755 3.7025
##
## Coefficients:
## Estimate Std. Error z value
## (Intercept) 1.991412 2.285603 0.871
## biddable 1.663804 0.202424 8.219
## D.ratio.nstopwrds.nwrds -1.316612 2.213100 -0.595
## D.npnct15.log 1.340396 1.088486 1.231
## D.T.screen -0.596517 0.774824 -0.770
## D.npnct03.log -0.471488 1.512259 -0.312
## D.T.used 0.094107 0.631360 0.149
## D.T.excellent 0.411714 0.414664 0.993
## D.T.great 0.236186 0.610025 0.387
## D.ratio.sum.TfIdf.nwrds -0.250916 0.438982 -0.572
## D.T.good 0.013422 0.625580 0.021
## D.npnct01.log -1.411432 0.893562 -1.580
## D.T.veri 0.026448 0.826339 0.032
## D.T.work 0.604670 0.754088 0.802
## D.T.scratch 0.408186 0.752332 0.543
## D.P.air -1.013709 1.029735 -0.984
## D.T.use 0.275408 0.921889 0.299
## storage.fctr16 -0.385483 0.531597 -0.725
## storage.fctr32 -0.026067 0.547501 -0.048
## storage.fctr64 0.082547 0.541935 0.152
## storage.fctrUnknown 0.664710 0.693948 0.958
## D.P.mini 1.136228 1.048031 1.084
## D.T.condition 0.694420 0.897298 0.774
## D.npnct11.log 0.454961 0.347014 1.311
## .rnorm -0.125352 0.096643 -1.297
## D.T.ipad 0.483505 0.927323 0.521
## D.npnct10.log 0.972999 1.799203 0.541
## D.sum.TfIdf 0.110638 0.150047 0.737
## D.T.new 1.815163 0.900403 2.016
## D.npnct13.log -0.367556 0.363557 -1.011
## D.npnct08.log -0.548680 0.745787 -0.736
## D.T.condit 0.203766 0.574528 0.355
## color.fctrBlack 0.173820 0.249447 0.697
## color.fctrGold 0.138107 0.582206 0.237
## `color.fctrSpace Gray` 0.204460 0.334470 0.611
## color.fctrWhite 0.350746 0.249900 1.404
## D.nstopwrds.log 0.841922 0.635379 1.325
## D.npnct16.log 3.171609 1.814439 1.748
## D.npnct24.log 0.965056 2.569251 0.376
## D.T.this -0.100361 1.132509 -0.089
## D.npnct06.log -3.459204 1.992381 -1.736
## D.T.box -0.952496 0.889028 -1.071
## D.npnct28.log -0.049196 2.192994 -0.022
## D.T.like -1.117442 0.821572 -1.360
## D.npnct12.log -0.792353 0.798547 -0.992
## D.nuppr.log -0.201537 0.519364 -0.388
## D.nchrs.log -0.194265 0.501887 -0.387
## D.nwrds.log -0.020754 0.739745 -0.028
## D.npnct09.log -1.732555 5.139365 -0.337
## D.nwrds.unq.log -0.858232 0.552457 -1.553
## D.ndgts.log 0.332924 0.448083 0.743
## `carrier.fctrAT&T` 0.232354 0.726143 0.320
## carrier.fctrOther 0.662862 1.900101 0.349
## carrier.fctrSprint 0.117004 0.953926 0.123
## `carrier.fctrT-Mobile` -0.359912 1.020340 -0.353
## carrier.fctrUnknown 0.483090 0.718737 0.672
## carrier.fctrVerizon 0.453471 0.751785 0.603
## cellular.fctr1 0.111153 0.699449 0.159
## cellular.fctrUnknown -0.572200 0.785487 -0.728
## D.npnct14.log -0.314827 0.859177 -0.366
## `prdline.my.fctriPad 2` 0.449728 0.330378 1.361
## `prdline.my.fctriPad 3` 0.908481 0.372486 2.439
## `prdline.my.fctriPad 4` 0.626103 0.423823 1.477
## `prdline.my.fctriPad 5` 0.000000 2.500000 0.000
## `prdline.my.fctriPad Air` 1.444492 0.456739 3.163
## `prdline.my.fctriPad Air 2` 2.888613 0.550730 5.245
## `prdline.my.fctriPad mini` 0.350776 0.330576 1.061
## `prdline.my.fctriPad mini 2` 1.386523 0.501865 2.763
## `prdline.my.fctriPad mini 3` 0.445529 0.684079 0.651
## `prdline.my.fctriPad mini Retina` 1.765515 0.967413 1.825
## prdline.my.fctrUnknown -0.725185 0.461802 -1.570
## D.npnct05.log -1.585515 1.415922 -1.120
## `condition.fctrFor parts or not working` -0.928539 0.338008 -2.747
## `condition.fctrManufacturer refurbished` 0.574266 0.736336 0.780
## condition.fctrNew -0.162513 0.342423 -0.475
## `condition.fctrNew other (see details)` -0.032576 0.492279 -0.066
## `condition.fctrSeller refurbished` -0.776439 0.421232 -1.843
## startprice -0.011019 0.001215 -9.067
## Pr(>|z|)
## (Intercept) 0.38360
## biddable < 2e-16 ***
## D.ratio.nstopwrds.nwrds 0.55190
## D.npnct15.log 0.21816
## D.T.screen 0.44137
## D.npnct03.log 0.75521
## D.T.used 0.88151
## D.T.excellent 0.32076
## D.T.great 0.69863
## D.ratio.sum.TfIdf.nwrds 0.56760
## D.T.good 0.98288
## D.npnct01.log 0.11421
## D.T.veri 0.97447
## D.T.work 0.42264
## D.T.scratch 0.58743
## D.P.air 0.32490
## D.T.use 0.76514
## storage.fctr16 0.46837
## storage.fctr32 0.96203
## storage.fctr64 0.87894
## storage.fctrUnknown 0.33813
## D.P.mini 0.27830
## D.T.condition 0.43899
## D.npnct11.log 0.18983
## .rnorm 0.19461
## D.T.ipad 0.60209
## D.npnct10.log 0.58865
## D.sum.TfIdf 0.46091
## D.T.new 0.04381 *
## D.npnct13.log 0.31202
## D.npnct08.log 0.46191
## D.T.condit 0.72284
## color.fctrBlack 0.48591
## color.fctrGold 0.81249
## `color.fctrSpace Gray` 0.54100
## color.fctrWhite 0.16045
## D.nstopwrds.log 0.18515
## D.npnct16.log 0.08047 .
## D.npnct24.log 0.70720
## D.T.this 0.92939
## D.npnct06.log 0.08253 .
## D.T.box 0.28399
## D.npnct28.log 0.98210
## D.T.like 0.17379
## D.npnct12.log 0.32108
## D.nuppr.log 0.69798
## D.nchrs.log 0.69870
## D.nwrds.log 0.97762
## D.npnct09.log 0.73603
## D.nwrds.unq.log 0.12031
## D.ndgts.log 0.45748
## `carrier.fctrAT&T` 0.74898
## carrier.fctrOther 0.72720
## carrier.fctrSprint 0.90238
## `carrier.fctrT-Mobile` 0.72429
## carrier.fctrUnknown 0.50150
## carrier.fctrVerizon 0.54638
## cellular.fctr1 0.87374
## cellular.fctrUnknown 0.46633
## D.npnct14.log 0.71405
## `prdline.my.fctriPad 2` 0.17343
## `prdline.my.fctriPad 3` 0.01473 *
## `prdline.my.fctriPad 4` 0.13960
## `prdline.my.fctriPad 5` 1.00000
## `prdline.my.fctriPad Air` 0.00156 **
## `prdline.my.fctriPad Air 2` 1.56e-07 ***
## `prdline.my.fctriPad mini` 0.28864
## `prdline.my.fctriPad mini 2` 0.00573 **
## `prdline.my.fctriPad mini 3` 0.51486
## `prdline.my.fctriPad mini Retina` 0.06800 .
## prdline.my.fctrUnknown 0.11634
## D.npnct05.log 0.26281
## `condition.fctrFor parts or not working` 0.00601 **
## `condition.fctrManufacturer refurbished` 0.43545
## condition.fctrNew 0.63507
## `condition.fctrNew other (see details)` 0.94724
## `condition.fctrSeller refurbished` 0.06529 .
## startprice < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1337.51 on 968 degrees of freedom
## Residual deviance: 794.34 on 891 degrees of freedom
## AIC: 950.34
##
## Number of Fisher Scoring iterations: 13
##
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.7184943
## 3 0.2 0.7629428
## 4 0.3 0.7815631
## 5 0.4 0.7918015
## 6 0.5 0.7986111
## 7 0.6 0.7927711
## 8 0.7 0.7708067
## 9 0.8 0.7085077
## 10 0.9 0.4482759
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.All.X.bayesglm.N
## 1 N 450
## 2 Y 102
## sold.fctr.predict.All.X.bayesglm.Y
## 1 72
## 2 345
## Prediction
## Reference N Y
## N 450 72
## Y 102 345
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 8.204334e-01 6.369521e-01 7.947886e-01 8.441134e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 5.071854e-76 2.791461e-02
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6736475
## 3 0.2 0.7048544
## 4 0.3 0.7186147
## 5 0.4 0.7363531
## 6 0.5 0.7336683
## 7 0.6 0.7326203
## 8 0.7 0.6971429
## 9 0.8 0.6204724
## 10 0.9 0.3831418
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.All.X.bayesglm.N
## 1 N 348
## 2 Y 96
## sold.fctr.predict.All.X.bayesglm.Y
## 1 131
## 2 317
## Prediction
## Reference N Y
## N 348 131
## Y 96 317
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.455157e-01 4.912002e-01 7.155892e-01 7.738105e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 8.982535e-38 2.402937e-02
## model_id model_method
## 1 All.X.bayesglm bayesglm
## feats
## 1 biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 2.381 0.269
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8942546 0.5 0.7986111 0.7678019
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7947886 0.8441134 0.5312525 0.819327
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.7363531 0.7455157
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1 0.7155892 0.7738105 0.4912002 950.3381
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.0233741 0.04896774
## label step_major step_minor bgn end elapsed
## 3 fit.models_1_bayesglm 3 0 75.369 80.922 5.553
## 4 fit.models_1_rpart 4 0 80.923 NA NA
## [1] "fitting model: All.X.no.rnorm.rpart"
## [1] " indep_vars: biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice"
## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.0157 on full training set## Warning in myfit_mdl(model_id = model_id, model_method = method,
## indep_vars_vctr = indep_vars_vctr, : model's bestTune found at an extreme
## of tuneGrid for parameter: cp
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 969
##
## CP nsplit rel error
## 1 0.52572707 0 1.0000000
## 2 0.01789709 1 0.4742729
## 3 0.01565996 3 0.4384787
##
## Variable importance
## biddable
## 51
## startprice
## 39
## condition.fctrNew
## 2
## condition.fctrFor parts or not working
## 2
## prdline.my.fctriPad Air 2
## 2
## D.npnct03.log
## 1
## color.fctrSpace Gray
## 1
## prdline.my.fctriPad Air
## 1
## prdline.my.fctriPad 2
## 1
## D.sum.TfIdf
## 1
## condition.fctrNew other (see details)
## 1
##
## Node number 1: 969 observations, complexity param=0.5257271
## predicted class=N expected loss=0.4613003 P(node) =1
## class counts: 522 447
## probabilities: 0.539 0.461
## left son=2 (530 obs) right son=3 (439 obs)
## Primary splits:
## biddable < 0.5 to the left, improve=150.656500, (0 missing)
## startprice < 126.475 to the right, improve=127.798500, (0 missing)
## condition.fctrNew < 0.5 to the right, improve= 21.222440, (0 missing)
## prdline.my.fctriPad mini 3 < 0.5 to the right, improve= 9.639246, (0 missing)
## D.ratio.nstopwrds.nwrds < 0.2071429 to the left, improve= 6.077179, (0 missing)
## Surrogate splits:
## startprice < 152.995 to the right, agree=0.760, adj=0.469, (0 split)
## condition.fctrFor parts or not working < 0.5 to the left, agree=0.562, adj=0.034, (0 split)
## D.npnct03.log < 0.3465736 to the left, agree=0.556, adj=0.021, (0 split)
## prdline.my.fctriPad 2 < 0.5 to the left, agree=0.554, adj=0.016, (0 split)
## D.sum.TfIdf < 7.685369 to the left, agree=0.553, adj=0.014, (0 split)
##
## Node number 2: 530 observations
## predicted class=N expected loss=0.2075472 P(node) =0.5469556
## class counts: 420 110
## probabilities: 0.792 0.208
##
## Node number 3: 439 observations, complexity param=0.01789709
## predicted class=Y expected loss=0.2323462 P(node) =0.4530444
## class counts: 102 337
## probabilities: 0.232 0.768
## left son=6 (154 obs) right son=7 (285 obs)
## Primary splits:
## startprice < 127.5 to the right, improve=39.114740, (0 missing)
## condition.fctrNew < 0.5 to the right, improve= 6.198332, (0 missing)
## prdline.my.fctriPad mini 3 < 0.5 to the right, improve= 2.813945, (0 missing)
## D.ratio.nstopwrds.nwrds < 0.1882353 to the left, improve= 2.510720, (0 missing)
## prdline.my.fctrUnknown < 0.5 to the right, improve= 2.194095, (0 missing)
## Surrogate splits:
## condition.fctrNew < 0.5 to the right, agree=0.706, adj=0.162, (0 split)
## prdline.my.fctriPad Air 2 < 0.5 to the right, agree=0.695, adj=0.130, (0 split)
## color.fctrSpace Gray < 0.5 to the right, agree=0.674, adj=0.071, (0 split)
## prdline.my.fctriPad Air < 0.5 to the right, agree=0.672, adj=0.065, (0 split)
## condition.fctrNew other (see details) < 0.5 to the right, agree=0.667, adj=0.052, (0 split)
##
## Node number 6: 154 observations, complexity param=0.01789709
## predicted class=N expected loss=0.4805195 P(node) =0.1589267
## class counts: 80 74
## probabilities: 0.519 0.481
## left son=12 (24 obs) right son=13 (130 obs)
## Primary splits:
## startprice < 414.995 to the right, improve=5.601066, (0 missing)
## D.T.use < 0.1281762 to the right, improve=2.608787, (0 missing)
## D.nstopwrds.log < 2.249905 to the right, improve=2.608787, (0 missing)
## D.nwrds.log < 2.970086 to the right, improve=2.608787, (0 missing)
## prdline.my.fctriPad 3 < 0.5 to the left, improve=2.593262, (0 missing)
## Surrogate splits:
## color.fctrGold < 0.5 to the right, agree=0.851, adj=0.042, (0 split)
## prdline.my.fctriPad mini 3 < 0.5 to the right, agree=0.851, adj=0.042, (0 split)
##
## Node number 7: 285 observations
## predicted class=Y expected loss=0.07719298 P(node) =0.2941176
## class counts: 22 263
## probabilities: 0.077 0.923
##
## Node number 12: 24 observations
## predicted class=N expected loss=0.1666667 P(node) =0.0247678
## class counts: 20 4
## probabilities: 0.833 0.167
##
## Node number 13: 130 observations
## predicted class=Y expected loss=0.4615385 P(node) =0.1341589
## class counts: 60 70
## probabilities: 0.462 0.538
##
## n= 969
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 969 447 N (0.53869969 0.46130031)
## 2) biddable< 0.5 530 110 N (0.79245283 0.20754717) *
## 3) biddable>=0.5 439 102 Y (0.23234624 0.76765376)
## 6) startprice>=127.5 154 74 N (0.51948052 0.48051948)
## 12) startprice>=414.995 24 4 N (0.83333333 0.16666667) *
## 13) startprice< 414.995 130 60 Y (0.46153846 0.53846154) *
## 7) startprice< 127.5 285 22 Y (0.07719298 0.92280702) *
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.6313559
## 3 0.2 0.6364943
## 4 0.3 0.7726218
## 5 0.4 0.7726218
## 6 0.5 0.7726218
## 7 0.6 0.7185792
## 8 0.7 0.7185792
## 9 0.8 0.7185792
## 10 0.9 0.7185792
## 11 1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.All.X.no.rnorm.rpart.N
## 1 N 440
## 2 Y 114
## sold.fctr.predict.All.X.no.rnorm.rpart.Y
## 1 82
## 2 333
## Prediction
## Reference N Y
## N 440 82
## Y 114 333
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.977296e-01 5.909173e-01 7.710339e-01 8.226019e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 1.071676e-63 2.680913e-02
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6329502
## 3 0.2 0.6320682
## 4 0.3 0.7478043
## 5 0.4 0.7478043
## 6 0.5 0.7478043
## 7 0.6 0.6706949
## 8 0.7 0.6706949
## 9 0.8 0.6706949
## 10 0.9 0.6706949
## 11 1.0 0.0000000## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.All.X.no.rnorm.rpart.N
## 1 N 393
## 2 Y 115
## sold.fctr.predict.All.X.no.rnorm.rpart.Y
## 1 86
## 2 298
## Prediction
## Reference N Y
## N 393 86
## Y 115 298
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.746637e-01 5.446437e-01 7.458018e-01 8.016983e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 3.787245e-49 4.827181e-02
## model_id model_method
## 1 All.X.no.rnorm.rpart rpart
## feats
## 1 biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 3 1.531 0.064
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.8255676 0.5 0.7726218 0.7853457
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.7710339 0.8226019 0.5603172 0.7965723
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.5 0.7478043 0.7746637
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.7458018 0.8016983 0.5446437
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.006444786 0.01305058
## label step_major step_minor bgn end elapsed
## 4 fit.models_1_rpart 4 0 80.923 86.07 5.147
## 5 fit.models_1_rf 5 0 86.071 NA NA
## [1] "fitting model: All.X.no.rnorm.rf"
## [1] " indep_vars: biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice"## Loading required package: randomForest
## randomForest 4.6-10
## Type rfNews() to see new features/changes/bug fixes.
##
## Attaching package: 'randomForest'
##
## The following object is masked from 'package:dplyr':
##
## combine
## Aggregating results
## Selecting tuning parameters
## Fitting mtry = 39 on full training set
## Length Class Mode
## call 4 -none- call
## type 1 -none- character
## predicted 969 factor numeric
## err.rate 1500 -none- numeric
## confusion 6 -none- numeric
## votes 1938 matrix numeric
## oob.times 969 -none- numeric
## classes 2 -none- character
## importance 76 -none- numeric
## importanceSD 0 -none- NULL
## localImportance 0 -none- NULL
## proximity 0 -none- NULL
## ntree 1 -none- numeric
## mtry 1 -none- numeric
## forest 14 -none- list
## y 969 factor numeric
## test 0 -none- NULL
## inbag 0 -none- NULL
## xNames 76 -none- character
## problemType 1 -none- character
## tuneValue 1 data.frame list
## obsLevels 2 -none- character
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6313559
## 2 0.1 0.8270120
## 3 0.2 0.9293139
## 4 0.3 0.9727965
## 5 0.4 0.9922309
## 6 0.5 0.9944259
## 7 0.6 0.9841270
## 8 0.7 0.9306220
## 9 0.8 0.8611465
## 10 0.9 0.7408451
## 11 1.0 0.1866126
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.All.X.no.rnorm.rf.N
## 1 N 518
## 2 Y 1
## sold.fctr.predict.All.X.no.rnorm.rf.Y
## 1 4
## 2 446
## Prediction
## Reference N Y
## N 518 4
## Y 1 446
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 9.948400e-01 9.896229e-01 9.879998e-01 9.983225e-01 5.386997e-01
## AccuracyPValue McnemarPValue
## 1.544343e-248 3.710934e-01
## [1] " calling mypredict_mdl for OOB:"
## threshold f.score
## 1 0.0 0.6329502
## 2 0.1 0.6603284
## 3 0.2 0.7098039
## 4 0.3 0.7351351
## 5 0.4 0.7458432
## 6 0.5 0.7373868
## 7 0.6 0.7154930
## 8 0.7 0.6706949
## 9 0.8 0.6240000
## 10 0.9 0.4964539
## 11 1.0 0.1438202
## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
## sold.fctr sold.fctr.predict.All.X.no.rnorm.rf.N
## 1 N 364
## 2 Y 99
## sold.fctr.predict.All.X.no.rnorm.rf.Y
## 1 115
## 2 314
## Prediction
## Reference N Y
## N 364 115
## Y 99 314
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.600897e-01 5.188223e-01 7.306732e-01 7.877768e-01 5.369955e-01
## AccuracyPValue McnemarPValue
## 3.092559e-43 3.051844e-01
## model_id model_method
## 1 All.X.no.rnorm.rf rf
## feats
## 1 biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 3 16.341 4.776
## max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.9998736 0.5 0.9944259 0.8070175
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1 0.9879998 0.9983225 0.608212 0.8221603
## opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1 0.4 0.7458432 0.7600897
## max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1 0.7306732 0.7877768 0.5188223
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.01814076 0.03737143# User specified
# Ensure at least 2 vars in each regression; else varImp crashes
# sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df; sav_featsimp_df <- glb_featsimp_df
# glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df; glm_featsimp_df <- sav_featsimp_df
# easier to exclude features
# require(gdata) # needed for trim
# model_id <- "";
# indep_vars_vctr <- head(subset(glb_models_df, grepl("All\\.X\\.", model_id), select=feats)
# , 1)[, "feats"]
# indep_vars_vctr <- trim(unlist(strsplit(indep_vars_vctr, "[,]")))
# indep_vars_vctr <- setdiff(indep_vars_vctr, ".rnorm")
# easier to include features
#model_id <- "Rank9.2"; indep_vars_vctr <- c(NULL
# ,"<feat1>"
# ,"<feat1>*<feat2>"
# ,"<feat1>:<feat2>"
# )
# for (method in c("bayesglm")) {
# ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# model_type=glb_model_type,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
# csm_mdl_id <- paste0(model_id, ".", method)
# csm_featsimp_df <- myget_feats_importance(glb_models_lst[[paste0(model_id, ".", method)]]); print(head(csm_featsimp_df))
# }
# Ntv.1.lm <- lm(reformulate(indep_vars_vctr, glb_rsp_var), glb_trnobs_df); print(summary(Ntv.1.lm))
#print(dsp_models_df <- orderBy(model_sel_frmla, glb_models_df)[, dsp_models_cols])
#csm_featsimp_df[grepl("H.npnct19.log", row.names(csm_featsimp_df)), , FALSE]
#csm_OOBobs_df <- glb_get_predictions(glb_OOBobs_df, mdl_id=csm_mdl_id, rsp_var_out=glb_rsp_var_out, prob_threshold_def=glb_models_df[glb_models_df$model_id == csm_mdl_id, "opt.prob.threshold.OOB"])
#print(sprintf("%s OOB confusion matrix & accuracy: ", csm_mdl_id)); print(t(confusionMatrix(csm_OOBobs_df[, paste0(glb_rsp_var_out, csm_mdl_id)], csm_OOBobs_df[, glb_rsp_var])$table))
#glb_models_df[, "max.Accuracy.OOB", FALSE]
#varImp(glb_models_lst[["Low.cor.X.glm"]])
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.2.glm"]])$importance)
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.3.glm"]])$importance)
#glb_feats_df[grepl("npnct28", glb_feats_df$id), ]
#print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id)); print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)], glb_OOBobs_df[, glb_rsp_var])$table))
# User specified bivariate models
# indep_vars_vctr_lst <- list()
# for (feat in setdiff(names(glb_fitobs_df),
# union(glb_rsp_var, glb_exclude_vars_as_features)))
# indep_vars_vctr_lst[["feat"]] <- feat
# User specified combinatorial models
# indep_vars_vctr_lst <- list()
# combn_mtrx <- combn(c("<feat1_name>", "<feat2_name>", "<featn_name>"),
# <num_feats_to_choose>)
# for (combn_ix in 1:ncol(combn_mtrx))
# #print(combn_mtrx[, combn_ix])
# indep_vars_vctr_lst[[combn_ix]] <- combn_mtrx[, combn_ix]
# template for myfit_mdl
# rf is hard-coded in caret to recognize only Accuracy / Kappa evaluation metrics
# only for OOB in trainControl ?
# ret_lst <- myfit_mdl_fn(model_id=paste0(model_id_pfx, ""), model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df,
# model_loss_mtrx=glb_model_metric_terms,
# model_summaryFunction=glb_model_metric_smmry,
# model_metric=glb_model_metric,
# model_metric_maximize=glb_model_metric_maximize)
# Simplify a model
# fit_df <- glb_fitobs_df; glb_mdl <- step(<complex>_mdl)
# Non-caret models
# rpart_area_mdl <- rpart(reformulate("Area", response=glb_rsp_var),
# data=glb_fitobs_df, #method="class",
# control=rpart.control(cp=0.12),
# parms=list(loss=glb_model_metric_terms))
# print("rpart_sel_wlm_mdl"); prp(rpart_sel_wlm_mdl)
#
print(glb_models_df)## model_id model_method
## MFO.myMFO_classfr MFO.myMFO_classfr myMFO_classfr
## Random.myrandom_classfr Random.myrandom_classfr myrandom_classfr
## Max.cor.Y.cv.0.rpart Max.cor.Y.cv.0.rpart rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart rpart
## Max.cor.Y.rpart Max.cor.Y.rpart rpart
## Max.cor.Y.glm Max.cor.Y.glm glm
## Interact.High.cor.Y.glm Interact.High.cor.Y.glm glm
## Low.cor.X.glm Low.cor.X.glm glm
## All.X.glm All.X.glm glm
## All.X.bayesglm All.X.bayesglm bayesglm
## All.X.no.rnorm.rpart All.X.no.rnorm.rpart rpart
## All.X.no.rnorm.rf All.X.no.rnorm.rf rf
## feats
## MFO.myMFO_classfr .rnorm
## Random.myrandom_classfr .rnorm
## Max.cor.Y.cv.0.rpart biddable, startprice
## Max.cor.Y.cv.0.cp.0.rpart biddable, startprice
## Max.cor.Y.rpart biddable, startprice
## Max.cor.Y.glm biddable, startprice
## Interact.High.cor.Y.glm biddable, startprice, biddable:D.nwrds.unq.log, biddable:D.T.like, biddable:D.npnct06.log, biddable:D.ratio.nstopwrds.nwrds, biddable:D.nchrs.log, biddable:D.nwrds.log, biddable:cellular.fctr
## Low.cor.X.glm biddable, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.npnct08.log, D.T.condit, color.fctr, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.glm biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.bayesglm biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.no.rnorm.rpart biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.no.rnorm.rf biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns min.elapsedtime.everything
## MFO.myMFO_classfr 0 0.387
## Random.myrandom_classfr 0 0.252
## Max.cor.Y.cv.0.rpart 0 0.679
## Max.cor.Y.cv.0.cp.0.rpart 0 0.470
## Max.cor.Y.rpart 3 0.949
## Max.cor.Y.glm 1 0.923
## Interact.High.cor.Y.glm 1 0.941
## Low.cor.X.glm 1 1.235
## All.X.glm 1 1.366
## All.X.bayesglm 1 2.381
## All.X.no.rnorm.rpart 3 1.531
## All.X.no.rnorm.rf 3 16.341
## min.elapsedtime.final max.auc.fit
## MFO.myMFO_classfr 0.003 0.5000000
## Random.myrandom_classfr 0.001 0.4877665
## Max.cor.Y.cv.0.rpart 0.011 0.5000000
## Max.cor.Y.cv.0.cp.0.rpart 0.008 0.8775832
## Max.cor.Y.rpart 0.011 0.8255676
## Max.cor.Y.glm 0.011 0.8592854
## Interact.High.cor.Y.glm 0.015 0.8593261
## Low.cor.X.glm 0.129 0.8890475
## All.X.glm 0.176 0.8974946
## All.X.bayesglm 0.269 0.8942546
## All.X.no.rnorm.rpart 0.064 0.8255676
## All.X.no.rnorm.rf 4.776 0.9998736
## opt.prob.threshold.fit max.f.score.fit
## MFO.myMFO_classfr 0.5 0.0000000
## Random.myrandom_classfr 0.4 0.6313559
## Max.cor.Y.cv.0.rpart 0.5 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.4 0.7977011
## Max.cor.Y.rpart 0.5 0.7726218
## Max.cor.Y.glm 0.4 0.7771679
## Interact.High.cor.Y.glm 0.4 0.7753304
## Low.cor.X.glm 0.5 0.7954023
## All.X.glm 0.5 0.8009153
## All.X.bayesglm 0.5 0.7986111
## All.X.no.rnorm.rpart 0.5 0.7726218
## All.X.no.rnorm.rf 0.5 0.9944259
## max.Accuracy.fit max.AccuracyLower.fit
## MFO.myMFO_classfr 0.5386997 0.5067192
## Random.myrandom_classfr 0.4613003 0.4295557
## Max.cor.Y.cv.0.rpart 0.5386997 0.5067192
## Max.cor.Y.cv.0.cp.0.rpart 0.8183695 0.7926235
## Max.cor.Y.rpart 0.7894737 0.7710339
## Max.cor.Y.glm 0.7915377 0.7635025
## Interact.High.cor.Y.glm 0.7894737 0.7624276
## Low.cor.X.glm 0.7636739 0.7904595
## All.X.glm 0.7574819 0.7947886
## All.X.bayesglm 0.7678019 0.7947886
## All.X.no.rnorm.rpart 0.7853457 0.7710339
## All.X.no.rnorm.rf 0.8070175 0.9879998
## max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## MFO.myMFO_classfr 0.5704443 0.0000000 0.5000000
## Random.myrandom_classfr 0.4932808 0.0000000 0.5196257
## Max.cor.Y.cv.0.rpart 0.5704443 0.0000000 0.5000000
## Max.cor.Y.cv.0.cp.0.rpart 0.8421635 0.6331346 0.7908880
## Max.cor.Y.rpart 0.8226019 0.5719410 0.7965723
## Max.cor.Y.glm 0.8157303 0.5781217 0.8223119
## Interact.High.cor.Y.glm 0.8147476 0.5739487 0.8220844
## Low.cor.X.glm 0.8402123 0.5225041 0.8242202
## All.X.glm 0.8441134 0.5103726 0.8156723
## All.X.bayesglm 0.8441134 0.5312525 0.8193270
## All.X.no.rnorm.rpart 0.8226019 0.5603172 0.7965723
## All.X.no.rnorm.rf 0.9983225 0.6082120 0.8221603
## opt.prob.threshold.OOB max.f.score.OOB
## MFO.myMFO_classfr 0.5 0.0000000
## Random.myrandom_classfr 0.4 0.6329502
## Max.cor.Y.cv.0.rpart 0.5 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.3 0.7294982
## Max.cor.Y.rpart 0.5 0.7478043
## Max.cor.Y.glm 0.5 0.7427854
## Interact.High.cor.Y.glm 0.4 0.7434679
## Low.cor.X.glm 0.4 0.7418605
## All.X.glm 0.4 0.7374562
## All.X.bayesglm 0.4 0.7363531
## All.X.no.rnorm.rpart 0.5 0.7478043
## All.X.no.rnorm.rf 0.4 0.7458432
## max.Accuracy.OOB max.AccuracyLower.OOB
## MFO.myMFO_classfr 0.5369955 0.5036362
## Random.myrandom_classfr 0.4630045 0.4298903
## Max.cor.Y.cv.0.rpart 0.5369955 0.5036362
## Max.cor.Y.cv.0.cp.0.rpart 0.7522422 0.7225457
## Max.cor.Y.rpart 0.7746637 0.7458018
## Max.cor.Y.glm 0.7701794 0.7411419
## Interact.High.cor.Y.glm 0.7578475 0.7283498
## Low.cor.X.glm 0.7511211 0.7213857
## All.X.glm 0.7477578 0.7179071
## All.X.bayesglm 0.7455157 0.7155892
## All.X.no.rnorm.rpart 0.7746637 0.7458018
## All.X.no.rnorm.rf 0.7600897 0.7306732
## max.AccuracyUpper.OOB max.Kappa.OOB
## MFO.myMFO_classfr 0.5701097 0.0000000
## Random.myrandom_classfr 0.4963638 0.0000000
## Max.cor.Y.cv.0.rpart 0.5701097 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.7802619 0.5010074
## Max.cor.Y.rpart 0.8016983 0.5446437
## Max.cor.Y.glm 0.7974197 0.5355819
## Interact.High.cor.Y.glm 0.7856310 0.5143253
## Low.cor.X.glm 0.7791873 0.5023247
## All.X.glm 0.7759620 0.4953483
## All.X.bayesglm 0.7738105 0.4912002
## All.X.no.rnorm.rpart 0.8016983 0.5446437
## All.X.no.rnorm.rf 0.7877768 0.5188223
## max.AccuracySD.fit max.KappaSD.fit min.aic.fit
## MFO.myMFO_classfr NA NA NA
## Random.myrandom_classfr NA NA NA
## Max.cor.Y.cv.0.rpart NA NA NA
## Max.cor.Y.cv.0.cp.0.rpart NA NA NA
## Max.cor.Y.rpart 0.009287926 0.01597718 NA
## Max.cor.Y.glm 0.012512235 0.02532251 912.5107
## Interact.High.cor.Y.glm 0.008191181 0.01641682 918.2717
## Low.cor.X.glm 0.017051302 0.03600209 934.6420
## All.X.glm 0.028766481 0.06032482 939.1513
## All.X.bayesglm 0.023374100 0.04896774 950.3381
## All.X.no.rnorm.rpart 0.006444786 0.01305058 NA
## All.X.no.rnorm.rf 0.018140759 0.03737143 NArm(ret_lst)
fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df, "fit.models_1_end",
major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 5 fit.models_1_rf 5 0 86.071 106.312 20.241
## 6 fit.models_1_end 6 0 106.313 NA NAglb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 11 fit.models 7 1 65.927 106.32 40.393
## 12 fit.models 7 2 106.320 NA NAif (!is.null(glb_model_metric_smmry)) {
stats_df <- glb_models_df[, "model_id", FALSE]
stats_mdl_df <- data.frame()
for (model_id in stats_df$model_id) {
stats_mdl_df <- rbind(stats_mdl_df,
mypredict_mdl(glb_models_lst[[model_id]], glb_fitobs_df, glb_rsp_var,
glb_rsp_var_out, model_id, "fit",
glb_model_metric_smmry, glb_model_metric,
glb_model_metric_maximize, ret_type="stats"))
}
stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
stats_mdl_df <- data.frame()
for (model_id in stats_df$model_id) {
stats_mdl_df <- rbind(stats_mdl_df,
mypredict_mdl(glb_models_lst[[model_id]], glb_OOBobs_df, glb_rsp_var,
glb_rsp_var_out, model_id, "OOB",
glb_model_metric_smmry, glb_model_metric,
glb_model_metric_maximize, ret_type="stats"))
}
stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
print("Merging following data into glb_models_df:")
print(stats_mrg_df <- stats_df[, c(1, grep(glb_model_metric, names(stats_df)))])
print(tmp_models_df <- orderBy(~model_id, glb_models_df[, c("model_id",
grep(glb_model_metric, names(stats_df), value=TRUE))]))
tmp2_models_df <- glb_models_df[, c("model_id", setdiff(names(glb_models_df),
grep(glb_model_metric, names(stats_df), value=TRUE)))]
tmp3_models_df <- merge(tmp2_models_df, stats_mrg_df, all.x=TRUE, sort=FALSE)
print(tmp3_models_df)
print(names(tmp3_models_df))
print(glb_models_df <- subset(tmp3_models_df, select=-model_id.1))
}
plt_models_df <- glb_models_df[, -grep("SD|Upper|Lower", names(glb_models_df))]
for (var in grep("^min.", names(plt_models_df), value=TRUE)) {
plt_models_df[, sub("min.", "inv.", var)] <-
#ifelse(all(is.na(tmp <- plt_models_df[, var])), NA, 1.0 / tmp)
1.0 / plt_models_df[, var]
plt_models_df <- plt_models_df[ , -grep(var, names(plt_models_df))]
}
print(plt_models_df)## model_id model_method
## MFO.myMFO_classfr MFO.myMFO_classfr myMFO_classfr
## Random.myrandom_classfr Random.myrandom_classfr myrandom_classfr
## Max.cor.Y.cv.0.rpart Max.cor.Y.cv.0.rpart rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart rpart
## Max.cor.Y.rpart Max.cor.Y.rpart rpart
## Max.cor.Y.glm Max.cor.Y.glm glm
## Interact.High.cor.Y.glm Interact.High.cor.Y.glm glm
## Low.cor.X.glm Low.cor.X.glm glm
## All.X.glm All.X.glm glm
## All.X.bayesglm All.X.bayesglm bayesglm
## All.X.no.rnorm.rpart All.X.no.rnorm.rpart rpart
## All.X.no.rnorm.rf All.X.no.rnorm.rf rf
## feats
## MFO.myMFO_classfr .rnorm
## Random.myrandom_classfr .rnorm
## Max.cor.Y.cv.0.rpart biddable, startprice
## Max.cor.Y.cv.0.cp.0.rpart biddable, startprice
## Max.cor.Y.rpart biddable, startprice
## Max.cor.Y.glm biddable, startprice
## Interact.High.cor.Y.glm biddable, startprice, biddable:D.nwrds.unq.log, biddable:D.T.like, biddable:D.npnct06.log, biddable:D.ratio.nstopwrds.nwrds, biddable:D.nchrs.log, biddable:D.nwrds.log, biddable:cellular.fctr
## Low.cor.X.glm biddable, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.npnct08.log, D.T.condit, color.fctr, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.glm biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.bayesglm biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, .rnorm, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.no.rnorm.rpart biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## All.X.no.rnorm.rf biddable, D.ratio.nstopwrds.nwrds, D.npnct15.log, D.T.screen, D.npnct03.log, D.T.used, D.T.excellent, D.T.great, D.ratio.sum.TfIdf.nwrds, D.T.good, D.npnct01.log, D.T.veri, D.T.work, D.T.scratch, D.P.air, D.T.use, storage.fctr, D.P.mini, D.T.condition, D.npnct11.log, D.T.ipad, D.npnct10.log, D.sum.TfIdf, D.T.new, D.npnct13.log, D.npnct08.log, D.T.condit, color.fctr, D.nstopwrds.log, D.npnct16.log, D.npnct24.log, D.T.this, D.npnct06.log, D.T.box, D.npnct28.log, D.T.like, D.npnct12.log, D.nuppr.log, D.nchrs.log, D.nwrds.log, D.npnct09.log, D.nwrds.unq.log, D.ndgts.log, carrier.fctr, cellular.fctr, D.npnct14.log, prdline.my.fctr, D.npnct05.log, condition.fctr, startprice
## max.nTuningRuns max.auc.fit
## MFO.myMFO_classfr 0 0.5000000
## Random.myrandom_classfr 0 0.4877665
## Max.cor.Y.cv.0.rpart 0 0.5000000
## Max.cor.Y.cv.0.cp.0.rpart 0 0.8775832
## Max.cor.Y.rpart 3 0.8255676
## Max.cor.Y.glm 1 0.8592854
## Interact.High.cor.Y.glm 1 0.8593261
## Low.cor.X.glm 1 0.8890475
## All.X.glm 1 0.8974946
## All.X.bayesglm 1 0.8942546
## All.X.no.rnorm.rpart 3 0.8255676
## All.X.no.rnorm.rf 3 0.9998736
## opt.prob.threshold.fit max.f.score.fit
## MFO.myMFO_classfr 0.5 0.0000000
## Random.myrandom_classfr 0.4 0.6313559
## Max.cor.Y.cv.0.rpart 0.5 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.4 0.7977011
## Max.cor.Y.rpart 0.5 0.7726218
## Max.cor.Y.glm 0.4 0.7771679
## Interact.High.cor.Y.glm 0.4 0.7753304
## Low.cor.X.glm 0.5 0.7954023
## All.X.glm 0.5 0.8009153
## All.X.bayesglm 0.5 0.7986111
## All.X.no.rnorm.rpart 0.5 0.7726218
## All.X.no.rnorm.rf 0.5 0.9944259
## max.Accuracy.fit max.Kappa.fit max.auc.OOB
## MFO.myMFO_classfr 0.5386997 0.0000000 0.5000000
## Random.myrandom_classfr 0.4613003 0.0000000 0.5196257
## Max.cor.Y.cv.0.rpart 0.5386997 0.0000000 0.5000000
## Max.cor.Y.cv.0.cp.0.rpart 0.8183695 0.6331346 0.7908880
## Max.cor.Y.rpart 0.7894737 0.5719410 0.7965723
## Max.cor.Y.glm 0.7915377 0.5781217 0.8223119
## Interact.High.cor.Y.glm 0.7894737 0.5739487 0.8220844
## Low.cor.X.glm 0.7636739 0.5225041 0.8242202
## All.X.glm 0.7574819 0.5103726 0.8156723
## All.X.bayesglm 0.7678019 0.5312525 0.8193270
## All.X.no.rnorm.rpart 0.7853457 0.5603172 0.7965723
## All.X.no.rnorm.rf 0.8070175 0.6082120 0.8221603
## opt.prob.threshold.OOB max.f.score.OOB
## MFO.myMFO_classfr 0.5 0.0000000
## Random.myrandom_classfr 0.4 0.6329502
## Max.cor.Y.cv.0.rpart 0.5 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.3 0.7294982
## Max.cor.Y.rpart 0.5 0.7478043
## Max.cor.Y.glm 0.5 0.7427854
## Interact.High.cor.Y.glm 0.4 0.7434679
## Low.cor.X.glm 0.4 0.7418605
## All.X.glm 0.4 0.7374562
## All.X.bayesglm 0.4 0.7363531
## All.X.no.rnorm.rpart 0.5 0.7478043
## All.X.no.rnorm.rf 0.4 0.7458432
## max.Accuracy.OOB max.Kappa.OOB
## MFO.myMFO_classfr 0.5369955 0.0000000
## Random.myrandom_classfr 0.4630045 0.0000000
## Max.cor.Y.cv.0.rpart 0.5369955 0.0000000
## Max.cor.Y.cv.0.cp.0.rpart 0.7522422 0.5010074
## Max.cor.Y.rpart 0.7746637 0.5446437
## Max.cor.Y.glm 0.7701794 0.5355819
## Interact.High.cor.Y.glm 0.7578475 0.5143253
## Low.cor.X.glm 0.7511211 0.5023247
## All.X.glm 0.7477578 0.4953483
## All.X.bayesglm 0.7455157 0.4912002
## All.X.no.rnorm.rpart 0.7746637 0.5446437
## All.X.no.rnorm.rf 0.7600897 0.5188223
## inv.elapsedtime.everything inv.elapsedtime.final
## MFO.myMFO_classfr 2.58397933 333.3333333
## Random.myrandom_classfr 3.96825397 1000.0000000
## Max.cor.Y.cv.0.rpart 1.47275405 90.9090909
## Max.cor.Y.cv.0.cp.0.rpart 2.12765957 125.0000000
## Max.cor.Y.rpart 1.05374078 90.9090909
## Max.cor.Y.glm 1.08342362 90.9090909
## Interact.High.cor.Y.glm 1.06269926 66.6666667
## Low.cor.X.glm 0.80971660 7.7519380
## All.X.glm 0.73206442 5.6818182
## All.X.bayesglm 0.41999160 3.7174721
## All.X.no.rnorm.rpart 0.65316786 15.6250000
## All.X.no.rnorm.rf 0.06119577 0.2093802
## inv.aic.fit
## MFO.myMFO_classfr NA
## Random.myrandom_classfr NA
## Max.cor.Y.cv.0.rpart NA
## Max.cor.Y.cv.0.cp.0.rpart NA
## Max.cor.Y.rpart NA
## Max.cor.Y.glm 0.001095878
## Interact.High.cor.Y.glm 0.001089002
## Low.cor.X.glm 0.001069928
## All.X.glm 0.001064791
## All.X.bayesglm 0.001052257
## All.X.no.rnorm.rpart NA
## All.X.no.rnorm.rf NAprint(myplot_radar(radar_inp_df=plt_models_df))## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.## Warning: Removed 4 rows containing missing values (geom_path).## Warning: Removed 87 rows containing missing values (geom_point).## Warning: Removed 7 rows containing missing values (geom_text).## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.
# print(myplot_radar(radar_inp_df=subset(plt_models_df,
# !(model_id %in% grep("random|MFO", plt_models_df$model_id, value=TRUE)))))
# Compute CI for <metric>SD
glb_models_df <- mutate(glb_models_df,
max.df = ifelse(max.nTuningRuns > 1, max.nTuningRuns - 1, NA),
min.sd2ci.scaler = ifelse(is.na(max.df), NA, qt(0.975, max.df)))
for (var in grep("SD", names(glb_models_df), value=TRUE)) {
# Does CI alredy exist ?
var_components <- unlist(strsplit(var, "SD"))
varActul <- paste0(var_components[1], var_components[2])
varUpper <- paste0(var_components[1], "Upper", var_components[2])
varLower <- paste0(var_components[1], "Lower", var_components[2])
if (varUpper %in% names(glb_models_df)) {
warning(varUpper, " already exists in glb_models_df")
# Assuming Lower also exists
next
}
print(sprintf("var:%s", var))
# CI is dependent on sample size in t distribution; df=n-1
glb_models_df[, varUpper] <- glb_models_df[, varActul] +
glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
glb_models_df[, varLower] <- glb_models_df[, varActul] -
glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
}## Warning: max.AccuracyUpper.fit already exists in glb_models_df## [1] "var:max.KappaSD.fit"# Plot metrics with CI
plt_models_df <- glb_models_df[, "model_id", FALSE]
pltCI_models_df <- glb_models_df[, "model_id", FALSE]
for (var in grep("Upper", names(glb_models_df), value=TRUE)) {
var_components <- unlist(strsplit(var, "Upper"))
col_name <- unlist(paste(var_components, collapse=""))
plt_models_df[, col_name] <- glb_models_df[, col_name]
for (name in paste0(var_components[1], c("Upper", "Lower"), var_components[2]))
pltCI_models_df[, name] <- glb_models_df[, name]
}
build_statsCI_data <- function(plt_models_df) {
mltd_models_df <- melt(plt_models_df, id.vars="model_id")
mltd_models_df$data <- sapply(1:nrow(mltd_models_df),
function(row_ix) tail(unlist(strsplit(as.character(
mltd_models_df[row_ix, "variable"]), "[.]")), 1))
mltd_models_df$label <- sapply(1:nrow(mltd_models_df),
function(row_ix) head(unlist(strsplit(as.character(
mltd_models_df[row_ix, "variable"]),
paste0(".", mltd_models_df[row_ix, "data"]))), 1))
#print(mltd_models_df)
return(mltd_models_df)
}
mltd_models_df <- build_statsCI_data(plt_models_df)
mltdCI_models_df <- melt(pltCI_models_df, id.vars="model_id")
for (row_ix in 1:nrow(mltdCI_models_df)) {
for (type in c("Upper", "Lower")) {
if (length(var_components <- unlist(strsplit(
as.character(mltdCI_models_df[row_ix, "variable"]), type))) > 1) {
#print(sprintf("row_ix:%d; type:%s; ", row_ix, type))
mltdCI_models_df[row_ix, "label"] <- var_components[1]
mltdCI_models_df[row_ix, "data"] <-
unlist(strsplit(var_components[2], "[.]"))[2]
mltdCI_models_df[row_ix, "type"] <- type
break
}
}
}
wideCI_models_df <- reshape(subset(mltdCI_models_df, select=-variable),
timevar="type",
idvar=setdiff(names(mltdCI_models_df), c("type", "value", "variable")),
direction="wide")
#print(wideCI_models_df)
mrgdCI_models_df <- merge(wideCI_models_df, mltd_models_df, all.x=TRUE)
#print(mrgdCI_models_df)
# Merge stats back in if CIs don't exist
goback_vars <- c()
for (var in unique(mltd_models_df$label)) {
for (type in unique(mltd_models_df$data)) {
var_type <- paste0(var, ".", type)
# if this data is already present, next
if (var_type %in% unique(paste(mltd_models_df$label, mltd_models_df$data,
sep=".")))
next
#print(sprintf("var_type:%s", var_type))
goback_vars <- c(goback_vars, var_type)
}
}
if (length(goback_vars) > 0) {
mltd_goback_df <- build_statsCI_data(glb_models_df[, c("model_id", goback_vars)])
mltd_models_df <- rbind(mltd_models_df, mltd_goback_df)
}
mltd_models_df <- merge(mltd_models_df, glb_models_df[, c("model_id", "model_method")],
all.x=TRUE)
png(paste0(glb_out_pfx, "models_bar.png"), width=480*3, height=480*2)
print(gp <- myplot_bar(mltd_models_df, "model_id", "value", colorcol_name="model_method") +
geom_errorbar(data=mrgdCI_models_df,
mapping=aes(x=model_id, ymax=value.Upper, ymin=value.Lower), width=0.5) +
facet_grid(label ~ data, scales="free") +
theme(axis.text.x = element_text(angle = 90,vjust = 0.5)))
dev.off()## quartz_off_screen
## 2print(gp)
# used for console inspection
model_evl_terms <- c(NULL)
for (metric in glb_model_evl_criteria)
model_evl_terms <- c(model_evl_terms,
ifelse(length(grep("max", metric)) > 0, "-", "+"), metric)
if (glb_is_classification && glb_is_binomial)
model_evl_terms <- c(model_evl_terms, "-", "opt.prob.threshold.OOB")
model_sel_frmla <- as.formula(paste(c("~ ", model_evl_terms), collapse=" "))
dsp_models_cols <- c("model_id", glb_model_evl_criteria)
if (glb_is_classification && glb_is_binomial)
dsp_models_cols <- c(dsp_models_cols, "opt.prob.threshold.OOB")
print(dsp_models_df <- orderBy(model_sel_frmla, glb_models_df)[, dsp_models_cols])## model_id max.Accuracy.OOB max.auc.OOB max.Kappa.OOB
## 5 Max.cor.Y.rpart 0.7746637 0.7965723 0.5446437
## 11 All.X.no.rnorm.rpart 0.7746637 0.7965723 0.5446437
## 6 Max.cor.Y.glm 0.7701794 0.8223119 0.5355819
## 12 All.X.no.rnorm.rf 0.7600897 0.8221603 0.5188223
## 7 Interact.High.cor.Y.glm 0.7578475 0.8220844 0.5143253
## 4 Max.cor.Y.cv.0.cp.0.rpart 0.7522422 0.7908880 0.5010074
## 8 Low.cor.X.glm 0.7511211 0.8242202 0.5023247
## 9 All.X.glm 0.7477578 0.8156723 0.4953483
## 10 All.X.bayesglm 0.7455157 0.8193270 0.4912002
## 1 MFO.myMFO_classfr 0.5369955 0.5000000 0.0000000
## 3 Max.cor.Y.cv.0.rpart 0.5369955 0.5000000 0.0000000
## 2 Random.myrandom_classfr 0.4630045 0.5196257 0.0000000
## min.aic.fit opt.prob.threshold.OOB
## 5 NA 0.5
## 11 NA 0.5
## 6 912.5107 0.5
## 12 NA 0.4
## 7 918.2717 0.4
## 4 NA 0.3
## 8 934.6420 0.4
## 9 939.1513 0.4
## 10 950.3381 0.4
## 1 NA 0.5
## 3 NA 0.5
## 2 NA 0.4print(myplot_radar(radar_inp_df=dsp_models_df))## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.## Warning: Removed 38 rows containing missing values (geom_point).## Warning: Removed 7 rows containing missing values (geom_text).## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.
print("Metrics used for model selection:"); print(model_sel_frmla)## [1] "Metrics used for model selection:"## ~-max.Accuracy.OOB - max.auc.OOB - max.Kappa.OOB + min.aic.fit -
## opt.prob.threshold.OOBprint(sprintf("Best model id: %s", dsp_models_df[1, "model_id"]))## [1] "Best model id: Max.cor.Y.rpart"if (is.null(glb_sel_mdl_id)) {
glb_sel_mdl_id <- dsp_models_df[1, "model_id"]
# if (glb_sel_mdl_id == "Interact.High.cor.Y.glm") {
# warning("glb_sel_mdl_id: Interact.High.cor.Y.glm; myextract_mdl_feats does not currently support interaction terms")
# glb_sel_mdl_id <- dsp_models_df[2, "model_id"]
# }
} else
print(sprintf("User specified selection: %s", glb_sel_mdl_id))
myprint_mdl(glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]])
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 969
##
## CP nsplit rel error
## 1 0.525727069 0 1.0000000
## 2 0.017897092 1 0.4742729
## 3 0.007270694 3 0.4384787
##
## Variable importance
## biddable startprice
## 57 43
##
## Node number 1: 969 observations, complexity param=0.5257271
## predicted class=N expected loss=0.4613003 P(node) =1
## class counts: 522 447
## probabilities: 0.539 0.461
## left son=2 (530 obs) right son=3 (439 obs)
## Primary splits:
## biddable < 0.5 to the left, improve=150.6565, (0 missing)
## startprice < 126.475 to the right, improve=127.7985, (0 missing)
## Surrogate splits:
## startprice < 152.995 to the right, agree=0.76, adj=0.469, (0 split)
##
## Node number 2: 530 observations
## predicted class=N expected loss=0.2075472 P(node) =0.5469556
## class counts: 420 110
## probabilities: 0.792 0.208
##
## Node number 3: 439 observations, complexity param=0.01789709
## predicted class=Y expected loss=0.2323462 P(node) =0.4530444
## class counts: 102 337
## probabilities: 0.232 0.768
## left son=6 (154 obs) right son=7 (285 obs)
## Primary splits:
## startprice < 127.5 to the right, improve=39.11474, (0 missing)
##
## Node number 6: 154 observations, complexity param=0.01789709
## predicted class=N expected loss=0.4805195 P(node) =0.1589267
## class counts: 80 74
## probabilities: 0.519 0.481
## left son=12 (24 obs) right son=13 (130 obs)
## Primary splits:
## startprice < 414.995 to the right, improve=5.601066, (0 missing)
##
## Node number 7: 285 observations
## predicted class=Y expected loss=0.07719298 P(node) =0.2941176
## class counts: 22 263
## probabilities: 0.077 0.923
##
## Node number 12: 24 observations
## predicted class=N expected loss=0.1666667 P(node) =0.0247678
## class counts: 20 4
## probabilities: 0.833 0.167
##
## Node number 13: 130 observations
## predicted class=Y expected loss=0.4615385 P(node) =0.1341589
## class counts: 60 70
## probabilities: 0.462 0.538
##
## n= 969
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 969 447 N (0.53869969 0.46130031)
## 2) biddable< 0.5 530 110 N (0.79245283 0.20754717) *
## 3) biddable>=0.5 439 102 Y (0.23234624 0.76765376)
## 6) startprice>=127.5 154 74 N (0.51948052 0.48051948)
## 12) startprice>=414.995 24 4 N (0.83333333 0.16666667) *
## 13) startprice< 414.995 130 60 Y (0.46153846 0.53846154) *
## 7) startprice< 127.5 285 22 Y (0.07719298 0.92280702) *## [1] TRUE# From here to save(), this should all be in one function
# these are executed in the same seq twice more:
# fit.data.training & predict.data.new chunks
glb_get_predictions <- function(df, mdl_id, rsp_var_out, prob_threshold_def=NULL) {
mdl <- glb_models_lst[[mdl_id]]
rsp_var_out <- paste0(rsp_var_out, mdl_id)
if (glb_is_regression) {
df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
print(myplot_scatter(df, glb_rsp_var, rsp_var_out, smooth=TRUE))
df[, paste0(rsp_var_out, ".err")] <-
abs(df[, rsp_var_out] - df[, glb_rsp_var])
print(head(orderBy(reformulate(c("-", paste0(rsp_var_out, ".err"))),
df)))
}
if (glb_is_classification && glb_is_binomial) {
prob_threshold <- glb_models_df[glb_models_df$model_id == mdl_id,
"opt.prob.threshold.OOB"]
if (is.null(prob_threshold) || is.na(prob_threshold)) {
warning("Using default probability threshold: ", prob_threshold_def)
if (is.null(prob_threshold <- prob_threshold_def))
stop("Default probability threshold is NULL")
}
df[, paste0(rsp_var_out, ".prob")] <-
predict(mdl, newdata=df, type="prob")[, 2]
df[, rsp_var_out] <-
factor(levels(df[, glb_rsp_var])[
(df[, paste0(rsp_var_out, ".prob")] >=
prob_threshold) * 1 + 1], levels(df[, glb_rsp_var]))
# prediction stats already reported by myfit_mdl ???
}
if (glb_is_classification && !glb_is_binomial) {
df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
df[, paste0(rsp_var_out, ".prob")] <-
predict(mdl, newdata=df, type="prob")
}
return(df)
}
glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id,
rsp_var_out=glb_rsp_var_out)
predct_accurate_var_name <- paste0(glb_rsp_var_out, glb_sel_mdl_id, ".accurate")
glb_OOBobs_df[, predct_accurate_var_name] <-
(glb_OOBobs_df[, glb_rsp_var] ==
glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)])
glb_featsimp_df <-
myget_feats_importance(mdl=glb_sel_mdl, featsimp_df=NULL)
glb_featsimp_df[, paste0(glb_sel_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)## importance Max.cor.Y.rpart.importance
## startprice 100 100
## biddable 0 0# Used again in fit.data.training & predict.data.new chunks
glb_analytics_diag_plots <- function(obs_df, mdl_id, prob_threshold=NULL) {
featsimp_df <- glb_featsimp_df
featsimp_df$feat <- gsub("`(.*?)`", "\\1", row.names(featsimp_df))
featsimp_df$feat.interact <- gsub("(.*?):(.*)", "\\2", featsimp_df$feat)
featsimp_df$feat <- gsub("(.*?):(.*)", "\\1", featsimp_df$feat)
featsimp_df$feat.interact <- ifelse(featsimp_df$feat.interact == featsimp_df$feat,
NA, featsimp_df$feat.interact)
featsimp_df$feat <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat)
featsimp_df$feat.interact <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat.interact)
featsimp_df <- orderBy(~ -importance.max, summaryBy(importance ~ feat + feat.interact,
data=featsimp_df, FUN=max))
#rex_str=":(.*)"; txt_vctr=tail(featsimp_df$feat); ret_lst <- regexec(rex_str, txt_vctr); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])
if (nrow(featsimp_df) > 5) {
warning("Limiting important feature scatter plots to 5 out of ", nrow(featsimp_df))
featsimp_df <- head(featsimp_df, 5)
}
# if (!all(is.na(featsimp_df$feat.interact)))
# stop("not implemented yet")
rsp_var_out <- paste0(glb_rsp_var_out, mdl_id)
for (var in featsimp_df$feat) {
plot_df <- melt(obs_df, id.vars=var,
measure.vars=c(glb_rsp_var, rsp_var_out))
# if (var == "<feat_name>") print(myplot_scatter(plot_df, var, "value",
# facet_colcol_name="variable") +
# geom_vline(xintercept=<divider_val>, linetype="dotted")) else
print(myplot_scatter(plot_df, var, "value", colorcol_name="variable",
facet_colcol_name="variable", jitter=TRUE) +
guides(color=FALSE))
}
if (glb_is_regression) {
if (nrow(featsimp_df) == 0)
warning("No important features in glb_fin_mdl") else
print(myplot_prediction_regression(df=obs_df,
feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2],
".rownames"),
feat_y=featsimp_df$feat[1],
rsp_var=glb_rsp_var, rsp_var_out=rsp_var_out,
id_vars=glb_id_var)
# + facet_wrap(reformulate(featsimp_df$feat[2])) # if [1 or 2] is a factor
# + geom_point(aes_string(color="<col_name>.fctr")) # to color the plot
)
}
if (glb_is_classification) {
if (nrow(featsimp_df) == 0)
warning("No features in selected model are statistically important")
else print(myplot_prediction_classification(df=obs_df,
feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2],
".rownames"),
feat_y=featsimp_df$feat[1],
rsp_var=glb_rsp_var,
rsp_var_out=rsp_var_out,
id_vars=glb_id_var,
prob_threshold=prob_threshold)
# + geom_hline(yintercept=<divider_val>, linetype = "dotted")
)
}
}
if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id) 
## [1] "Min/Max Boundaries: "
## UniqueID sold.fctr sold.fctr.predict.Max.cor.Y.rpart.prob
## 27 10027 Y 0.2075472
## 68 10068 Y 0.2075472
## 328 10328 Y 0.2075472
## 763 10763 Y 0.2075472
## 875 10875 Y 0.2075472
## 1535 11535 Y 0.2075472
## 20 10020 N 0.2075472
## 1283 11283 N 0.2075472
## 631 10631 Y 0.9228070
## 801 10801 N 0.5384615
## 941 10941 N 0.5384615
## 182 10182 N 0.9228070
## 526 10526 N 0.9228070
## 841 10841 N 0.9228070
## 1622 11622 N 0.9228070
## sold.fctr.predict.Max.cor.Y.rpart
## 27 N
## 68 N
## 328 N
## 763 N
## 875 N
## 1535 N
## 20 N
## 1283 N
## 631 Y
## 801 Y
## 941 Y
## 182 Y
## 526 Y
## 841 Y
## 1622 Y
## sold.fctr.predict.Max.cor.Y.rpart.accurate
## 27 FALSE
## 68 FALSE
## 328 FALSE
## 763 FALSE
## 875 FALSE
## 1535 FALSE
## 20 TRUE
## 1283 TRUE
## 631 TRUE
## 801 FALSE
## 941 FALSE
## 182 FALSE
## 526 FALSE
## 841 FALSE
## 1622 FALSE
## sold.fctr.predict.Max.cor.Y.rpart.error .label
## 27 -0.29245283 10027
## 68 -0.29245283 10068
## 328 -0.29245283 10328
## 763 -0.29245283 10763
## 875 -0.29245283 10875
## 1535 -0.29245283 11535
## 20 0.00000000 10020
## 1283 0.00000000 11283
## 631 0.00000000 10631
## 801 0.03846154 10801
## 941 0.03846154 10941
## 182 0.42280702 10182
## 526 0.42280702 10526
## 841 0.42280702 10841
## 1622 0.42280702 11622
## [1] "Inaccurate: "
## UniqueID sold.fctr sold.fctr.predict.Max.cor.Y.rpart.prob
## 297 10297 Y 0.1666667
## 775 10775 Y 0.1666667
## 1042 11042 Y 0.1666667
## 1053 11053 Y 0.1666667
## 1300 11300 Y 0.1666667
## 27 10027 Y 0.2075472
## sold.fctr.predict.Max.cor.Y.rpart
## 297 N
## 775 N
## 1042 N
## 1053 N
## 1300 N
## 27 N
## sold.fctr.predict.Max.cor.Y.rpart.accurate
## 297 FALSE
## 775 FALSE
## 1042 FALSE
## 1053 FALSE
## 1300 FALSE
## 27 FALSE
## sold.fctr.predict.Max.cor.Y.rpart.error
## 297 -0.3333333
## 775 -0.3333333
## 1042 -0.3333333
## 1053 -0.3333333
## 1300 -0.3333333
## 27 -0.2924528
## UniqueID sold.fctr sold.fctr.predict.Max.cor.Y.rpart.prob
## 1173 11173 Y 0.2075472
## 683 10683 N 0.5384615
## 1004 11004 N 0.5384615
## 1622 11622 N 0.9228070
## 567 10567 N 0.9228070
## 1700 11700 N 0.9228070
## sold.fctr.predict.Max.cor.Y.rpart
## 1173 N
## 683 Y
## 1004 Y
## 1622 Y
## 567 Y
## 1700 Y
## sold.fctr.predict.Max.cor.Y.rpart.accurate
## 1173 FALSE
## 683 FALSE
## 1004 FALSE
## 1622 FALSE
## 567 FALSE
## 1700 FALSE
## sold.fctr.predict.Max.cor.Y.rpart.error
## 1173 -0.29245283
## 683 0.03846154
## 1004 0.03846154
## 1622 0.42280702
## 567 0.42280702
## 1700 0.42280702
## UniqueID sold.fctr sold.fctr.predict.Max.cor.Y.rpart.prob
## 1704 11704 N 0.922807
## 413 10413 N 0.922807
## 1243 11243 N 0.922807
## 1602 11602 N 0.922807
## 1700 11700 N 0.922807
## 1769 11769 N 0.922807
## sold.fctr.predict.Max.cor.Y.rpart
## 1704 Y
## 413 Y
## 1243 Y
## 1602 Y
## 1700 Y
## 1769 Y
## sold.fctr.predict.Max.cor.Y.rpart.accurate
## 1704 FALSE
## 413 FALSE
## 1243 FALSE
## 1602 FALSE
## 1700 FALSE
## 1769 FALSE
## sold.fctr.predict.Max.cor.Y.rpart.error
## 1704 0.422807
## 413 0.422807
## 1243 0.422807
## 1602 0.422807
## 1700 0.422807
## 1769 0.422807
# gather predictions from models better than MFO.*
#mdl_id <- "Conditional.X.rf"
#mdl_id <- "Conditional.X.cp.0.rpart"
#mdl_id <- "Conditional.X.rpart"
# glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id,
# glb_rsp_var_out)
# print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, mdl_id)],
# glb_OOBobs_df[, glb_rsp_var])$table))
# FN_OOB_ids <- c(4721, 4020, 693, 92)
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# glb_feats_df$id[1:5]])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# glb_txt_vars])
write.csv(glb_OOBobs_df[, c(glb_id_var,
grep(glb_rsp_var, names(glb_OOBobs_df), fixed=TRUE, value=TRUE))],
paste0(gsub(".", "_", paste0(glb_out_pfx, glb_sel_mdl_id), fixed=TRUE),
"_OOBobs.csv"), row.names=FALSE)
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% FN_OOB_ids,
# glb_txt_vars])
# dsp_tbl(Headline.contains="[Ee]bola")
# sum(sel_obs(Headline.contains="[Ee]bola"))
# ftable(xtabs(Popular ~ NewsDesk.fctr, data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,]))
# xtabs(NewsDesk ~ Popular, #Popular ~ NewsDesk.fctr,
# data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,],
# exclude=NULL)
# print(mycreate_xtab_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,],
# tbl_col_names=c("Popular", "NewsDesk")))
# write.csv(glb_chunks_df, paste0(glb_out_pfx, tail(glb_chunks_df, 1)$label, "_",
# tail(glb_chunks_df, 1)$step_minor, "_chunks1.csv"),
# row.names=FALSE)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 12 fit.models 7 2 106.32 119.769 13.449
## 13 fit.models 7 3 119.77 NA NA if (sum(is.na(glb_allobs_df$D.P.http)) > 0)
stop("fit.models_3: Why is this happening ?")## Warning in is.na(glb_allobs_df$D.P.http): is.na() applied to non-(list or
## vector) of type 'NULL'#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))## [1] "sold.fctr.predict.Max.cor.Y.rpart.prob"
## [2] "sold.fctr.predict.Max.cor.Y.rpart"
## [3] "sold.fctr.predict.Max.cor.Y.rpart.accurate"for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))## character(0)if (glb_save_envir)
save(glb_feats_df,
glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_sel_mdl, glb_sel_mdl_id,
glb_model_type,
file=paste0(glb_out_pfx, "selmdl_dsk.RData"))
#load(paste0(glb_out_pfx, "selmdl_dsk.RData"))
rm(ret_lst)## Warning in rm(ret_lst): object 'ret_lst' not foundreplay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"model.selected")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
## 2.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction firing: model.selected
## 3.0000 3 0 2 1 0
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 13 fit.models 7 3 119.770 123.636 3.866
## 14 fit.data.training 8 0 123.636 NA NAStep 8.0: fit data training
#load(paste0(glb_inp_pfx, "dsk.RData"))
if (sum(is.na(glb_allobs_df$D.P.http)) > 0)
stop("fit.data.training_0: Why is this happening ?")## Warning in is.na(glb_allobs_df$D.P.http): is.na() applied to non-(list or
## vector) of type 'NULL'# To create specific models
# glb_fin_mdl_id <- NULL; glb_fin_mdl <- NULL;
# glb_sel_mdl_id <- "Conditional.X.cp.0.rpart";
# glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]]; print(glb_sel_mdl)
if (!is.null(glb_fin_mdl_id) && (glb_fin_mdl_id %in% names(glb_models_lst))) {
warning("Final model same as user selected model")
glb_fin_mdl <- glb_sel_mdl
} else {
# print(mdl_feats_df <- myextract_mdl_feats(sel_mdl=glb_sel_mdl,
# entity_df=glb_fitobs_df))
if ((model_method <- glb_sel_mdl$method) == "custom")
# get actual method from the model_id
model_method <- tail(unlist(strsplit(glb_sel_mdl_id, "[.]")), 1)
tune_finmdl_df <- NULL
if (nrow(glb_sel_mdl$bestTune) > 0) {
for (param in names(glb_sel_mdl$bestTune)) {
#print(sprintf("param: %s", param))
if (glb_sel_mdl$bestTune[1, param] != "none")
tune_finmdl_df <- rbind(tune_finmdl_df,
data.frame(parameter=param,
min=glb_sel_mdl$bestTune[1, param],
max=glb_sel_mdl$bestTune[1, param],
by=1)) # by val does not matter
}
}
# Sync with parameters in mydsutils.R
require(gdata)
ret_lst <- myfit_mdl(model_id="Final", model_method=model_method,
indep_vars_vctr=trim(unlist(strsplit(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"feats"], "[,]"))),
model_type=glb_model_type,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_trnobs_df, OOB_df=NULL,
n_cv_folds=glb_n_cv_folds, tune_models_df=tune_finmdl_df,
# Automate from here
# Issues if glb_sel_mdl$method == "rf" b/c trainControl is "oob"; not "cv"
model_loss_mtrx=glb_model_metric_terms,
model_summaryFunction=glb_sel_mdl$control$summaryFunction,
model_metric=glb_sel_mdl$metric,
model_metric_maximize=glb_sel_mdl$maximize)
glb_fin_mdl <- glb_models_lst[[length(glb_models_lst)]]
glb_fin_mdl_id <- glb_models_df[length(glb_models_lst), "model_id"]
}## Loading required package: gdata
## gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
##
## gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
##
## Attaching package: 'gdata'
##
## The following object is masked from 'package:randomForest':
##
## combine
##
## The following objects are masked from 'package:dplyr':
##
## combine, first, last
##
## The following object is masked from 'package:stats':
##
## nobs
##
## The following object is masked from 'package:utils':
##
## object.size## [1] "fitting model: Final.rpart"
## [1] " indep_vars: biddable, startprice"
## Aggregating results
## Fitting final model on full training set
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 1861
##
## CP nsplit rel error
## 1 0.515116279 0 1.0000000
## 2 0.011627907 1 0.4848837
## 3 0.007270694 3 0.4616279
##
## Variable importance
## biddable startprice
## 59 41
##
## Node number 1: 1861 observations, complexity param=0.5151163
## predicted class=N expected loss=0.4621171 P(node) =1
## class counts: 1001 860
## probabilities: 0.538 0.462
## left son=2 (1024 obs) right son=3 (837 obs)
## Primary splits:
## biddable < 0.5 to the left, improve=278.4233, (0 missing)
## startprice < 100.5 to the right, improve=214.6830, (0 missing)
## Surrogate splits:
## startprice < 100.5 to the right, agree=0.75, adj=0.443, (0 split)
##
## Node number 2: 1024 observations
## predicted class=N expected loss=0.2148438 P(node) =0.5502418
## class counts: 804 220
## probabilities: 0.785 0.215
##
## Node number 3: 837 observations, complexity param=0.01162791
## predicted class=Y expected loss=0.2353644 P(node) =0.4497582
## class counts: 197 640
## probabilities: 0.235 0.765
## left son=6 (295 obs) right son=7 (542 obs)
## Primary splits:
## startprice < 139.995 to the right, improve=62.99321, (0 missing)
##
## Node number 6: 295 observations, complexity param=0.01162791
## predicted class=Y expected loss=0.4983051 P(node) =0.1585169
## class counts: 147 148
## probabilities: 0.498 0.502
## left son=12 (38 obs) right son=13 (257 obs)
## Primary splits:
## startprice < 413.495 to the right, improve=6.11944, (0 missing)
##
## Node number 7: 542 observations
## predicted class=Y expected loss=0.09225092 P(node) =0.2912413
## class counts: 50 492
## probabilities: 0.092 0.908
##
## Node number 12: 38 observations
## predicted class=N expected loss=0.2368421 P(node) =0.02041913
## class counts: 29 9
## probabilities: 0.763 0.237
##
## Node number 13: 257 observations
## predicted class=Y expected loss=0.459144 P(node) =0.1380978
## class counts: 118 139
## probabilities: 0.459 0.541
##
## n= 1861
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 1861 860 N (0.53788286 0.46211714)
## 2) biddable< 0.5 1024 220 N (0.78515625 0.21484375) *
## 3) biddable>=0.5 837 197 Y (0.23536440 0.76463560)
## 6) startprice>=139.995 295 147 Y (0.49830508 0.50169492)
## 12) startprice>=413.495 38 9 N (0.76315789 0.23684211) *
## 13) startprice< 413.495 257 118 Y (0.45914397 0.54085603) *
## 7) startprice< 139.995 542 50 Y (0.09225092 0.90774908) *
## [1] " calling mypredict_mdl for fit:"
## threshold f.score
## 1 0.0 0.6321205
## 2 0.1 0.6321205
## 3 0.2 0.6321205
## 4 0.3 0.7606992
## 5 0.4 0.7606992
## 6 0.5 0.7606992
## 7 0.6 0.7018545
## 8 0.7 0.7018545
## 9 0.8 0.7018545
## 10 0.9 0.7018545
## 11 1.0 0.0000000## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
## sold.fctr sold.fctr.predict.Final.rpart.N
## 1 N 833
## 2 Y 229
## sold.fctr.predict.Final.rpart.Y
## 1 168
## 2 631
## Prediction
## Reference N Y
## N 833 168
## Y 229 631
## Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 7.866738e-01 5.687299e-01 7.673485e-01 8.050912e-01 5.378829e-01
## AccuracyPValue McnemarPValue
## 1.194566e-110 2.601200e-03## Warning in mypredict_mdl(mdl, df = fit_df, rsp_var, rsp_var_out,
## model_id_method, : Expecting 1 metric: Accuracy; recd: Accuracy, Kappa;
## retaining Accuracy only
## model_id model_method feats max.nTuningRuns
## 1 Final.rpart rpart biddable, startprice 1
## min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1 0.982 0.015 0.8131247
## opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1 0.5 0.7606992 0.7802279
## max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit
## 1 0.7673485 0.8050912 0.5532193
## max.AccuracySD.fit max.KappaSD.fit
## 1 0.0165079 0.03542625rm(ret_lst)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 14 fit.data.training 8 0 123.636 128.431 4.795
## 15 fit.data.training 8 1 128.431 NA NA#```
#```{r fit.data.training_1, cache=FALSE}
glb_trnobs_df <- glb_get_predictions(df=glb_trnobs_df, mdl_id=glb_fin_mdl_id,
rsp_var_out=glb_rsp_var_out,
prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial,
glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, "opt.prob.threshold.OOB"], NULL))## Warning in glb_get_predictions(df = glb_trnobs_df, mdl_id =
## glb_fin_mdl_id, : Using default probability threshold: 0.5sav_featsimp_df <- glb_featsimp_df
#glb_feats_df <- sav_feats_df
# glb_feats_df <- mymerge_feats_importance(feats_df=glb_feats_df, sel_mdl=glb_fin_mdl,
# entity_df=glb_trnobs_df)
glb_featsimp_df <- myget_feats_importance(mdl=glb_fin_mdl, featsimp_df=glb_featsimp_df)
glb_featsimp_df[, paste0(glb_fin_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)## Max.cor.Y.rpart.importance importance Final.rpart.importance
## startprice 100 100 100
## biddable 0 0 0if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id) 
## [1] "Min/Max Boundaries: "
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## 3 10003 Y 0.2148438
## 11 10011 Y 0.2148438
## 14 10014 Y 0.2148438
## 15 10015 Y 0.2148438
## 17 10017 Y 0.2148438
## 19 10019 Y 0.2148438
## 92 10092 Y 0.2368421
## 1 10001 N 0.2148438
## 2 10002 Y 0.9077491
## 91 10091 Y 0.9077491
## 1397 11397 N 0.2148438
## 103 10103 N 0.5408560
## 112 10112 N 0.5408560
## 120 10120 N 0.5408560
## 135 10135 N 0.5408560
## 127 10127 N 0.9077491
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## 3 N FALSE
## 11 N FALSE
## 14 N FALSE
## 15 N FALSE
## 17 N FALSE
## 19 N FALSE
## 92 N FALSE
## 1 N TRUE
## 2 Y TRUE
## 91 Y TRUE
## 1397 N TRUE
## 103 Y FALSE
## 112 Y FALSE
## 120 Y FALSE
## 135 Y FALSE
## 127 Y FALSE
## sold.fctr.predict.Final.rpart.error .label
## 3 -0.28515625 10003
## 11 -0.28515625 10011
## 14 -0.28515625 10014
## 15 -0.28515625 10015
## 17 -0.28515625 10017
## 19 -0.28515625 10019
## 92 -0.26315789 10092
## 1 0.00000000 10001
## 2 0.00000000 10002
## 91 0.00000000 10091
## 1397 0.00000000 11397
## 103 0.04085603 10103
## 112 0.04085603 10112
## 120 0.04085603 10120
## 135 0.04085603 10135
## 127 0.40774908 10127
## [1] "Inaccurate: "
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## 3 10003 Y 0.2148438
## 11 10011 Y 0.2148438
## 14 10014 Y 0.2148438
## 15 10015 Y 0.2148438
## 17 10017 Y 0.2148438
## 19 10019 Y 0.2148438
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## 3 N FALSE
## 11 N FALSE
## 14 N FALSE
## 15 N FALSE
## 17 N FALSE
## 19 N FALSE
## sold.fctr.predict.Final.rpart.error
## 3 -0.2851562
## 11 -0.2851562
## 14 -0.2851562
## 15 -0.2851562
## 17 -0.2851562
## 19 -0.2851562
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## 686 10686 Y 0.2148438
## 962 10962 Y 0.2148438
## 297 10297 Y 0.2368421
## 602 10602 N 0.5408560
## 1777 11777 N 0.5408560
## 416 10416 N 0.9077491
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## 686 N FALSE
## 962 N FALSE
## 297 N FALSE
## 602 Y FALSE
## 1777 Y FALSE
## 416 Y FALSE
## sold.fctr.predict.Final.rpart.error
## 686 -0.28515625
## 962 -0.28515625
## 297 -0.26315789
## 602 0.04085603
## 1777 0.04085603
## 416 0.40774908
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## 1718 11718 N 0.9077491
## 1741 11741 N 0.9077491
## 1748 11748 N 0.9077491
## 1769 11769 N 0.9077491
## 1796 11796 N 0.9077491
## 1836 11836 N 0.9077491
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## 1718 Y FALSE
## 1741 Y FALSE
## 1748 Y FALSE
## 1769 Y FALSE
## 1796 Y FALSE
## 1836 Y FALSE
## sold.fctr.predict.Final.rpart.error
## 1718 0.4077491
## 1741 0.4077491
## 1748 0.4077491
## 1769 0.4077491
## 1796 0.4077491
## 1836 0.4077491
dsp_feats_vctr <- c(NULL)
for(var in grep(".importance", names(glb_feats_df), fixed=TRUE, value=TRUE))
dsp_feats_vctr <- union(dsp_feats_vctr,
glb_feats_df[!is.na(glb_feats_df[, var]), "id"])
# print(glb_trnobs_df[glb_trnobs_df$UniqueID %in% FN_OOB_ids,
# grep(glb_rsp_var, names(glb_trnobs_df), value=TRUE)])
print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))## [1] "sold.fctr.predict.Final.rpart.prob"
## [2] "sold.fctr.predict.Final.rpart"for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]
print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))## character(0)for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))## character(0)if (glb_save_envir)
save(glb_feats_df, glb_allobs_df,
#glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
glb_sel_mdl, glb_sel_mdl_id,
glb_fin_mdl, glb_fin_mdl_id,
file=paste0(glb_out_pfx, "dsk.RData"))
replay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"data.training.all.prediction","model.final")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
## 2.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction firing: model.selected
## 3.0000 3 0 2 1 0
## 3.0000 multiple enabled transitions: model.final data.training.all.prediction data.new.prediction firing: data.training.all.prediction
## 4.0000 5 0 1 1 1
## 4.0000 multiple enabled transitions: model.final data.training.all.prediction data.new.prediction firing: model.final
## 5.0000 4 0 0 2 1
glb_chunks_df <- myadd_chunk(glb_chunks_df, "predict.data.new", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 15 fit.data.training 8 1 128.431 131.535 3.104
## 16 predict.data.new 9 0 131.535 NA NAStep 9.0: predict data new
# Compute final model predictions
# sav_newobs_df <- glb_newobs_df
glb_newobs_df <- glb_get_predictions(glb_newobs_df, mdl_id=glb_fin_mdl_id,
rsp_var_out=glb_rsp_var_out,
prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial,
glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"], NULL))## Warning in glb_get_predictions(glb_newobs_df, mdl_id = glb_fin_mdl_id,
## rsp_var_out = glb_rsp_var_out, : Using default probability threshold: 0.5if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id) ## Warning in min(x): no non-missing arguments to min; returning Inf## Warning in max(x): no non-missing arguments to max; returning -Inf## Warning: Removed 798 rows containing missing values (geom_point).## Warning: Removed 798 rows containing missing values (geom_point).
## Warning in min(x): no non-missing arguments to min; returning Inf## Warning in max(x): no non-missing arguments to max; returning -Inf## Warning: Removed 798 rows containing missing values (geom_point).## Warning: Removed 798 rows containing missing values (geom_point).
## [1] "Min/Max Boundaries: "
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## 1862 11862 <NA> 0.2148438
## 1865 11865 <NA> 0.9077491
## 1891 11891 <NA> 0.9077491
## 2625 12625 <NA> 0.2148438
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## 1862 N NA
## 1865 Y NA
## 1891 Y NA
## 2625 N NA
## sold.fctr.predict.Final.rpart.error .label
## 1862 0 11862
## 1865 0 11865
## 1891 0 11891
## 2625 0 12625
## [1] "Inaccurate: "
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## NA NA <NA> NA
## NA.1 NA <NA> NA
## NA.2 NA <NA> NA
## NA.3 NA <NA> NA
## NA.4 NA <NA> NA
## NA.5 NA <NA> NA
## sold.fctr.predict.Final.rpart sold.fctr.predict.Final.rpart.accurate
## NA <NA> NA
## NA.1 <NA> NA
## NA.2 <NA> NA
## NA.3 <NA> NA
## NA.4 <NA> NA
## NA.5 <NA> NA
## sold.fctr.predict.Final.rpart.error
## NA NA
## NA.1 NA
## NA.2 NA
## NA.3 NA
## NA.4 NA
## NA.5 NA
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## NA.264 NA <NA> NA
## NA.289 NA <NA> NA
## NA.453 NA <NA> NA
## NA.566 NA <NA> NA
## NA.602 NA <NA> NA
## NA.645 NA <NA> NA
## sold.fctr.predict.Final.rpart
## NA.264 <NA>
## NA.289 <NA>
## NA.453 <NA>
## NA.566 <NA>
## NA.602 <NA>
## NA.645 <NA>
## sold.fctr.predict.Final.rpart.accurate
## NA.264 NA
## NA.289 NA
## NA.453 NA
## NA.566 NA
## NA.602 NA
## NA.645 NA
## sold.fctr.predict.Final.rpart.error
## NA.264 NA
## NA.289 NA
## NA.453 NA
## NA.566 NA
## NA.602 NA
## NA.645 NA
## UniqueID sold.fctr sold.fctr.predict.Final.rpart.prob
## NA.792 NA <NA> NA
## NA.793 NA <NA> NA
## NA.794 NA <NA> NA
## NA.795 NA <NA> NA
## NA.796 NA <NA> NA
## NA.797 NA <NA> NA
## sold.fctr.predict.Final.rpart
## NA.792 <NA>
## NA.793 <NA>
## NA.794 <NA>
## NA.795 <NA>
## NA.796 <NA>
## NA.797 <NA>
## sold.fctr.predict.Final.rpart.accurate
## NA.792 NA
## NA.793 NA
## NA.794 NA
## NA.795 NA
## NA.796 NA
## NA.797 NA
## sold.fctr.predict.Final.rpart.error
## NA.792 NA
## NA.793 NA
## NA.794 NA
## NA.795 NA
## NA.796 NA
## NA.797 NA## Warning: Removed 798 rows containing missing values (geom_point).
if (glb_is_classification && glb_is_binomial) {
submit_df <- glb_newobs_df[, c(glb_id_var,
paste0(glb_rsp_var_out, glb_fin_mdl_id, ".prob"))]
names(submit_df)[2] <- "Probability1"
# submit_df <- glb_newobs_df[, c(paste0(glb_rsp_var_out, glb_fin_mdl_id)), FALSE]
# names(submit_df)[1] <- "BDscience"
# submit_df$BDscience <- as.numeric(submit_df$BDscience) - 1
# #submit_df <-rbind(submit_df, data.frame(bdanalytics=c(" ")))
# print("Submission Stats:")
# print(table(submit_df$BDscience, useNA = "ifany"))
} else submit_df <- glb_newobs_df[, c(glb_id_var,
paste0(glb_rsp_var_out, glb_fin_mdl_id))]
submit_fname <- paste0(gsub(".", "_", paste0(glb_out_pfx, glb_fin_mdl_id), fixed=TRUE),
"_submit.csv")
write.csv(submit_df, submit_fname, quote=FALSE, row.names=FALSE)
#cat(" ", "\n", file=submit_fn, append=TRUE)
# print(orderBy(~ -max.auc.OOB, glb_models_df[, c("model_id",
# "max.auc.OOB", "max.Accuracy.OOB")]))
if (glb_is_classification && glb_is_binomial)
print(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"])## [1] 0.5print(sprintf("glb_sel_mdl_id: %s", glb_sel_mdl_id))## [1] "glb_sel_mdl_id: Max.cor.Y.rpart"print(sprintf("glb_fin_mdl_id: %s", glb_fin_mdl_id))## [1] "glb_fin_mdl_id: Final.rpart"print(dim(glb_fitobs_df))## [1] 969 63print(dsp_models_df)## model_id max.Accuracy.OOB max.auc.OOB max.Kappa.OOB
## 5 Max.cor.Y.rpart 0.7746637 0.7965723 0.5446437
## 11 All.X.no.rnorm.rpart 0.7746637 0.7965723 0.5446437
## 6 Max.cor.Y.glm 0.7701794 0.8223119 0.5355819
## 12 All.X.no.rnorm.rf 0.7600897 0.8221603 0.5188223
## 7 Interact.High.cor.Y.glm 0.7578475 0.8220844 0.5143253
## 4 Max.cor.Y.cv.0.cp.0.rpart 0.7522422 0.7908880 0.5010074
## 8 Low.cor.X.glm 0.7511211 0.8242202 0.5023247
## 9 All.X.glm 0.7477578 0.8156723 0.4953483
## 10 All.X.bayesglm 0.7455157 0.8193270 0.4912002
## 1 MFO.myMFO_classfr 0.5369955 0.5000000 0.0000000
## 3 Max.cor.Y.cv.0.rpart 0.5369955 0.5000000 0.0000000
## 2 Random.myrandom_classfr 0.4630045 0.5196257 0.0000000
## min.aic.fit opt.prob.threshold.OOB
## 5 NA 0.5
## 11 NA 0.5
## 6 912.5107 0.5
## 12 NA 0.4
## 7 918.2717 0.4
## 4 NA 0.3
## 8 934.6420 0.4
## 9 939.1513 0.4
## 10 950.3381 0.4
## 1 NA 0.5
## 3 NA 0.5
## 2 NA 0.4if (glb_is_regression) {
print(sprintf("%s OOB RMSE: %0.4f", glb_sel_mdl_id,
glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, "min.RMSE.OOB"]))
if (!is.null(glb_category_vars)) {
stop("not implemented yet")
tmp_OOBobs_df <- glb_OOBobs_df[, c(glb_category_vars, predct_accurate_var_name)]
names(tmp_OOBobs_df)[length(names(tmp_OOBobs_df))] <- "accurate.OOB"
aOOB_ctgry_df <- mycreate_xtab_df(tmp_OOBobs_df, names(tmp_OOBobs_df))
aOOB_ctgry_df[is.na(aOOB_ctgry_df)] <- 0
aOOB_ctgry_df <- mutate(aOOB_ctgry_df,
.n.OOB = accurate.OOB.FALSE + accurate.OOB.TRUE,
max.accuracy.OOB = accurate.OOB.TRUE / .n.OOB)
#intersect(names(glb_ctgry_df), names(aOOB_ctgry_df))
glb_ctgry_df <- merge(glb_ctgry_df, aOOB_ctgry_df, all=TRUE)
print(orderBy(~-accurate.OOB.FALSE, glb_ctgry_df))
}
if ((glb_rsp_var %in% names(glb_newobs_df)) &&
!(any(is.na(glb_newobs_df[, glb_rsp_var])))) {
pred_stats_df <-
mypredict_mdl(mdl=glb_models_lst[[glb_fin_mdl_id]],
df=glb_newobs_df,
rsp_var=glb_rsp_var,
rsp_var_out=glb_rsp_var_out,
model_id_method=glb_fin_mdl_id,
label="new",
model_summaryFunction=glb_sel_mdl$control$summaryFunction,
model_metric=glb_sel_mdl$metric,
model_metric_maximize=glb_sel_mdl$maximize,
ret_type="stats")
print(sprintf("%s prediction stats for glb_newobs_df:", glb_fin_mdl_id))
print(pred_stats_df)
}
}
if (glb_is_classification) {
print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id))
print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)],
glb_OOBobs_df[, glb_rsp_var])$table))
if (!is.null(glb_category_vars)) {
tmp_OOBobs_df <- glb_OOBobs_df[, c(glb_category_vars, predct_accurate_var_name)]
names(tmp_OOBobs_df)[length(names(tmp_OOBobs_df))] <- "accurate.OOB"
aOOB_ctgry_df <- mycreate_xtab_df(tmp_OOBobs_df, names(tmp_OOBobs_df))
aOOB_ctgry_df[is.na(aOOB_ctgry_df)] <- 0
aOOB_ctgry_df <- mutate(aOOB_ctgry_df,
.n.OOB = accurate.OOB.FALSE + accurate.OOB.TRUE,
max.accuracy.OOB = accurate.OOB.TRUE / .n.OOB)
#intersect(names(glb_ctgry_df), names(aOOB_ctgry_df))
glb_ctgry_df <- merge(glb_ctgry_df, aOOB_ctgry_df, all=TRUE)
print(orderBy(~-accurate.OOB.FALSE, glb_ctgry_df))
}
if ((glb_rsp_var %in% names(glb_newobs_df)) &&
!(any(is.na(glb_newobs_df[, glb_rsp_var])))) {
print(sprintf("%s new confusion matrix & accuracy: ", glb_fin_mdl_id))
print(t(confusionMatrix(glb_newobs_df[, paste0(glb_rsp_var_out, glb_fin_mdl_id)],
glb_newobs_df[, glb_rsp_var])$table))
}
} ## [1] "Max.cor.Y.rpart OOB confusion matrix & accuracy: "
## Prediction
## Reference N Y
## N 393 86
## Y 115 298
## prdline.my .n.OOB .n.Tst .freqRatio.Tst .freqRatio.OOB
## 8 iPad mini 126 114 0.14285714 0.141255605
## 2 iPad 2 171 154 0.19298246 0.191704036
## 12 Unknown 97 87 0.10902256 0.108744395
## 1 iPad 1 99 89 0.11152882 0.110986547
## 3 iPad 3 61 55 0.06892231 0.068385650
## 4 iPad 4 76 68 0.08521303 0.085201794
## 9 iPad mini 2 63 56 0.07017544 0.070627803
## 7 iPad Air 2 69 62 0.07769424 0.077354260
## 6 iPad Air 84 75 0.09398496 0.094170404
## 10 iPad mini 3 43 38 0.04761905 0.048206278
## 11 iPad mini Retina 2 NA NA 0.002242152
## 5 iPad 5 1 NA NA 0.001121076
## accurate.OOB.FALSE accurate.OOB.TRUE max.accuracy.OOB
## 8 36 90 0.7142857
## 2 35 136 0.7953216
## 12 24 73 0.7525773
## 1 18 81 0.8181818
## 3 17 44 0.7213115
## 4 17 59 0.7763158
## 9 16 47 0.7460317
## 7 15 54 0.7826087
## 6 12 72 0.8571429
## 10 10 33 0.7674419
## 11 1 1 0.5000000
## 5 0 1 1.0000000dsp_myCategory_conf_mtrx <- function(myCategory) {
print(sprintf("%s OOB::myCategory=%s confusion matrix & accuracy: ",
glb_sel_mdl_id, myCategory))
print(t(confusionMatrix(
glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory,
paste0(glb_rsp_var_out, glb_sel_mdl_id)],
glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, glb_rsp_var])$table))
print(sum(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory,
predct_accurate_var_name]) /
nrow(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, ]))
err_ids <- glb_OOBobs_df[(glb_OOBobs_df$myCategory == myCategory) &
(!glb_OOBobs_df[, predct_accurate_var_name]), glb_id_var]
OOB_FNerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) &
(glb_OOBobs_df$Popular == 1),
c(
".clusterid",
"Popular", "Headline", "Snippet", "Abstract")]
print(sprintf("%s OOB::myCategory=%s FN errors: %d", glb_sel_mdl_id, myCategory,
nrow(OOB_FNerr_df)))
print(OOB_FNerr_df)
OOB_FPerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) &
(glb_OOBobs_df$Popular == 0),
c(
".clusterid",
"Popular", "Headline", "Snippet", "Abstract")]
print(sprintf("%s OOB::myCategory=%s FP errors: %d", glb_sel_mdl_id, myCategory,
nrow(OOB_FPerr_df)))
print(OOB_FPerr_df)
}
#dsp_myCategory_conf_mtrx(myCategory="OpEd#Opinion#")
#dsp_myCategory_conf_mtrx(myCategory="Business#Business Day#Dealbook")
#dsp_myCategory_conf_mtrx(myCategory="##")
# if (glb_is_classification) {
# print("FN_OOB_ids:")
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# glb_txt_vars])
# print(dsp_vctr <- colSums(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# setdiff(grep("[HSA].", names(glb_OOBobs_df), value=TRUE),
# union(myfind_chr_cols_df(glb_OOBobs_df),
# grep(".fctr", names(glb_OOBobs_df), fixed=TRUE, value=TRUE)))]))
# }
dsp_hdlpfx_results <- function(hdlpfx) {
print(hdlpfx)
print(glb_OOBobs_df[glb_OOBobs_df$Headline.pfx %in% c(hdlpfx),
grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
grep(glb_rsp_var, names(glb_newobs_df), value=TRUE)])
print(dsp_vctr <- colSums(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
setdiff(grep("[HSA]\\.", names(glb_newobs_df), value=TRUE),
union(myfind_chr_cols_df(glb_newobs_df),
grep(".fctr", names(glb_newobs_df), fixed=TRUE, value=TRUE)))]))
print(dsp_vctr <- dsp_vctr[dsp_vctr != 0])
print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
union(names(dsp_vctr), myfind_chr_cols_df(glb_newobs_df))])
}
#dsp_hdlpfx_results(hdlpfx="Ask Well::")
# print("myMisc::|OpEd|blank|blank|1:")
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% c(6446),
# grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# c("WordCount", "WordCount.log", "myMultimedia",
# "NewsDesk", "SectionName", "SubsectionName")])
# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"), ],
# c(glb_rsp_var, "myMultimedia")))
# dsp_chisq.test(Headline.contains="[Vi]deo")
# print(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"),
# c(glb_rsp_var, "Popular", "myMultimedia", "Headline")])
# print(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola", Popular=1),
# c(glb_rsp_var, "Popular", "myMultimedia", "Headline",
# "NewsDesk", "SectionName", "SubsectionName")])
# print(subset(glb_feats_df, !is.na(importance))[,
# c("is.ConditionalX.y",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.ConditionalX.y & is.na(importance))[,
# c("is.ConditionalX.y",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, !is.na(importance))[,
# c("zeroVar", "nzv", "myNearZV",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.na(importance))[,
# c("zeroVar", "nzv", "myNearZV",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
print(orderBy(as.formula(paste0("~ -", glb_sel_mdl_id, ".importance")), glb_featsimp_df))## Max.cor.Y.rpart.importance importance Final.rpart.importance
## startprice 100 100 100
## biddable 0 0 0print("glb_newobs_df prediction stats:")## [1] "glb_newobs_df prediction stats:"print(myplot_histogram(glb_newobs_df, paste0(glb_rsp_var_out, glb_fin_mdl_id)))
if (glb_is_classification)
print(table(glb_newobs_df[, paste0(glb_rsp_var_out, glb_fin_mdl_id)]))##
## N Y
## 439 359# players_df <- data.frame(id=c("Chavez", "Giambi", "Menechino", "Myers", "Pena"),
# OBP=c(0.338, 0.391, 0.369, 0.313, 0.361),
# SLG=c(0.540, 0.450, 0.374, 0.447, 0.500),
# cost=c(1400000, 1065000, 295000, 800000, 300000))
# players_df$RS.predict <- predict(glb_models_lst[[csm_mdl_id]], players_df)
# print(orderBy(~ -RS.predict, players_df))
if (length(diff <- setdiff(names(glb_trnobs_df), names(glb_allobs_df))) > 0)
print(diff)
for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]
if (length(diff <- setdiff(names(glb_fitobs_df), names(glb_allobs_df))) > 0)
print(diff)
if (length(diff <- setdiff(names(glb_OOBobs_df), names(glb_allobs_df))) > 0)
print(diff)
for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
if (length(diff <- setdiff(names(glb_newobs_df), names(glb_allobs_df))) > 0)
print(diff)
if (glb_save_envir)
save(glb_feats_df, glb_allobs_df,
#glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
glb_sel_mdl, glb_sel_mdl_id,
glb_fin_mdl, glb_fin_mdl_id,
file=paste0(glb_out_pfx, "prdnew_dsk.RData"))
rm(submit_df, tmp_OOBobs_df)
# tmp_replay_lst <- replay.petrisim(pn=glb_analytics_pn,
# replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
# "data.new.prediction")), flip_coord=TRUE)
# print(ggplot.petrinet(tmp_replay_lst[["pn"]]) + coord_flip())
glb_chunks_df <- myadd_chunk(glb_chunks_df, "display.session.info", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 16 predict.data.new 9 0 131.535 134.904 3.369
## 17 display.session.info 10 0 134.904 NA NANull Hypothesis (\(\sf{H_{0}}\)): mpg is not impacted by am_fctr.
The variance by am_fctr appears to be independent. #{r q1, cache=FALSE} # print(t.test(subset(cars_df, am_fctr == "automatic")$mpg, # subset(cars_df, am_fctr == "manual")$mpg, # var.equal=FALSE)$conf) # We reject the null hypothesis i.e. we have evidence to conclude that am_fctr impacts mpg (95% confidence). Manual transmission is better for miles per gallon versus automatic transmission.
## label step_major step_minor bgn end elapsed
## 11 fit.models 7 1 65.927 106.320 40.393
## 10 fit.models 7 0 41.384 65.926 24.542
## 5 extract.features 3 0 16.448 37.899 21.451
## 12 fit.models 7 2 106.320 119.769 13.449
## 2 inspect.data 2 0 10.248 15.538 5.290
## 14 fit.data.training 8 0 123.636 128.431 4.795
## 13 fit.models 7 3 119.770 123.636 3.866
## 16 predict.data.new 9 0 131.535 134.904 3.369
## 15 fit.data.training 8 1 128.431 131.535 3.104
## 8 select.features 5 0 38.973 40.432 1.460
## 9 partition.data.training 6 0 40.433 41.384 0.951
## 6 cluster.data 4 0 37.900 38.828 0.928
## 3 scrub.data 2 1 15.538 16.366 0.828
## 1 import.data 1 0 9.832 10.247 0.416
## 7 manage.missing.data 4 1 38.829 38.973 0.144
## 4 transform.data 2 2 16.367 16.448 0.081
## duration
## 11 40.393
## 10 24.542
## 5 21.451
## 12 13.449
## 2 5.290
## 14 4.795
## 13 3.866
## 16 3.369
## 15 3.104
## 8 1.459
## 9 0.951
## 6 0.928
## 3 0.828
## 1 0.415
## 7 0.144
## 4 0.081
## [1] "Total Elapsed Time: 134.904 secs"
## R version 3.2.1 (2015-06-18)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.10.4 (Yosemite)
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] tcltk grid parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] gdata_2.17.0 randomForest_4.6-10 arm_1.8-6
## [4] lme4_1.1-8 Matrix_1.2-2 MASS_7.3-42
## [7] rpart.plot_1.5.2 rpart_4.1-10 ROCR_1.0-7
## [10] gplots_2.17.0 sampling_2.7 tm_0.6-2
## [13] NLP_0.1-8 stringr_1.0.0 dplyr_0.4.2
## [16] plyr_1.8.3 sqldf_0.4-10 RSQLite_1.0.0
## [19] DBI_0.3.1 gsubfn_0.6-6 proto_0.3-10
## [22] reshape2_1.4.1 doMC_1.3.3 iterators_1.0.7
## [25] foreach_1.4.2 doBy_4.5-13 survival_2.38-3
## [28] caret_6.0-47 ggplot2_1.0.1 lattice_0.20-33
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.11.6 class_7.3-13 gtools_3.5.0
## [4] assertthat_0.1 digest_0.6.8 slam_0.1-32
## [7] R6_2.1.0 BradleyTerry2_1.0-6 chron_2.3-47
## [10] coda_0.17-1 evaluate_0.7 e1071_1.6-4
## [13] lazyeval_0.1.10 minqa_1.2.4 SparseM_1.6
## [16] car_2.0-25 nloptr_1.0.4 rmarkdown_0.7
## [19] labeling_0.3 splines_3.2.1 munsell_0.4.2
## [22] compiler_3.2.1 mgcv_1.8-6 htmltools_0.2.6
## [25] nnet_7.3-10 lpSolve_5.6.11 codetools_0.2-14
## [28] brglm_0.5-9 bitops_1.0-6 nlme_3.1-121
## [31] gtable_0.1.2 magrittr_1.5 formatR_1.2
## [34] scales_0.2.5 KernSmooth_2.23-15 stringi_0.5-5
## [37] RColorBrewer_1.1-2 tools_3.2.1 abind_1.4-3
## [40] pbkrtest_0.4-2 yaml_2.1.13 colorspace_1.2-6
## [43] caTools_1.17.1 knitr_1.10.5 quantreg_5.11